I have been messing around with 2 different ways of EQing my Distorted Guitars.
 
1st. Double track (85% L/R slightly different amp settings for both) send thru a bus then use EQ on the bus.
EQ is set with a high pass filter and low pass filter then I find the sweet spot in the lower range, usually around 400 to 600hz then drop it -3.0
 
2nd. Double track (85% L/R slightly different amp settings for both), I do not use a bus this time. Instead I EQ the left guitar with a high pass and low pass filter find the mid range sweet spot and drop it -3.0. The right guitar is EQ the same way but instead of finding the mid range I find the higher range, which seems to be around 900 to 1100hz then push it up +3.0.
 
The question is, which way is better, or is it just a personal preference type of thing? Or am I going about this all wrong?

it's a personal thing.
 
me, i never eq guitars, IF i can get the sound i want with the amp and the mic.
 
moving the mic is the best eq you can buy.
 
 
 
that said, experimenting to find unique sounds is way cool, and it puts your personal identification on the sound
 
 
the trick is, to know what sounds good or not.
or better, or worse.
 
i would never just automatically double track something, or split it a certain way, or eq it a certain way, just because it's a 'method'
 
 
always do these things to serve the song.
 
that's why there are no templates...
no rules....
no presets......
no formula
 

Regardless of the technique, the ultimate goal is to end up with subtle but distinguishable differences between the two tracks. This is what tells your brain to interpret the combination as being "wide", as if different elements are coming from different directions. EQ is the easiest and safest (read: mono-compatible) method, and applies to clean or distorted, electric or acoustic.
 
Bat's right, of course, about getting good tone at the source (and Bat does know guitar tone). But that's separate from the topic at hand. You can't always know in advance, as you're recording the tracks, exactly how they're going to fit together in the mix. That's where EQ and other tricks may come into play during the mixing stage.
 
To address the original question, yes it's a personal preference and depends on the effect you're after. You might want to experiment with more complex EQ curves, a graphic equalizer, or comb filters. If you have Voxengo's GlissEQ, it has a unique harmonic series filter option that's fun for this kind of thing. You can even try two flangers with different modulation speeds, preferably as a subtle parallel effect. 
 
Most of the time, you'll want to start off with complementary settings: whatever you do to the left side, you do exactly the opposite to the right side (except rolling off the low end, which should be the same on both sides).  The idea is that when the two tracks are added together they still represent the full spectrum.
 
Finally, you can apply a stereo widener on the bus. Stick to comb filtering algorithms rather than phase manipulation, M/S balance or delays.  Meldaproduction's MStereoSpread and PSP's StereoEnhancer are two plugins that provide this feature.
 

There is also no reason to stick to a hard fast rule of any particular pan rate (85%) seems far for all 4 tracks in this case....
Try this just for fun...
Take your take 1 (and a either play it twice, use 2 mics when tracking for different tones, or duplicate it as you were)  Eq them either separately or on a bus, and pan one 60% Left and the other say 70-80% left.  Often the one more towards the center I will EQ with more bottom end  and have the highs rolled off more than the other & the one that's out will have a little more of the mid-high end information.   
  Take your take #2 and do the same on the opposite side.   Also you can make those contrasting cuts/boosts as needed and desired between your left pair & right pair.  This will sound wider/fuller than what you are doing now because:
a) You have 2 different performances one clearly from one side and the other from the opposite side.  The human element and timing variations is perceived by the brain and it registers as far fatter than 4 copies of the same one take.
b)  You can EQ to accentuate the best parts of each take, find the frequencies in your tone that make that guitar what it is and let them shine.  Remove the mud!
c)  Instead of having your guitars all at 85% and similar info from left and right all the time you have differing performances on each side and a fatter wall of music.
   You had:  Guitar1@85%L<-------------------------------------------------0--------------------------------------------------------->Guitar 1@85%R
                  Guitar 2@85%L<-------------------------------------------------0-------------------------------------------------------->Guitar 2@85%R
 
This is: Guitar1/mic1 80%L<-----------Guitar1/mic2@60%L<---------------0---------------> Guitar2/mic1@60%R-------------->Guitar2/mic2@80%R
 
You can play around with how far out or in, Eq's, reverbs can set a part to the back of a mix, Compressors (though you don't need much if any on distorted guitars as they are already comped by the distortion, speaker, and mic) can put it right in your face. 
I have had distorted guitars that I highpassed as low as 75hz and others that got lopped off at around 130hz because I needed the room for other elements and they were getting in my way.   There are no set rules, mix for THAT song.  I like to roll my highs off a bit too as you mentioned above.  Sometimes as low as 7 or 8K (maybe on the inner pair in the above example) or for say a less-than-vital rhythm  track to leave some room for a lead/rhythm part above it somewhere around 9-12k  ??   Every track and every song is different.   I hope this helps you some dude!
Take care.

Hopefully the guitarist is eqing his guitar before it gets to the mic to match the song.  I mean, that is his job, to fit the guitar in.
 
That being said, I'll often filter the guitar just to be sure it is out of the way of the low and top end, compacting it a bit.  Why, I've even been known to further shape the guitar w/ dips and peaks once all the overdubbing is finished.  But these are small changes of a few dB - nothing dramatic. 
 
@

I think if you can help the person shape their tone with the guitar and amp that is best, then with mic position,  If you are having to boost/cut by more than 3 or 4 Db in the mix (other than the high/low pass) I think ya kinda failed at the tracking stage unless guitars were the 1st things laid down and you had never heard the song before.... you should have some idea of the tonality you are going for on the way in.

Hey guys, thanks for all the replies and advice. I decided to stick to double tracking having both track EQed differently. Changed my paning back to what it was when I started this album, 80%L 80%R. However I have a new slight problem with my lead tone. I have have found 4 harsh spots, 2260, 3311, 4170, 5159 I have taken them all down 1.5 with a Q of 12. It seems to have helped, I am wondering where all this harshness is coming from? Poor amp simulator (amplitube 3)? My hardware, old DOD FX7 pedal thru a Soundblaster Audigy gamer extreme sound card (yes I know, trust me, it hurt just to type that out lol)? Or, just bad playing on my part?

Edited.... because I can be a jerk off sometimes.  Sorry.

Fendicator
However I have a new slight problem with my lead tone. I have have found 4 harsh spots, 2260, 3311, 4170, 5159 I have taken them all down 1.5 with a Q of 12. It seems to have helped, I am wondering where all this harshness is coming from? Poor amp simulator (amplitube 3)? My hardware, old DOD FX7 pedal thru a Soundblaster Audigy gamer extreme sound card (yes I know, trust me, it hurt just to type that out lol)? Or, just bad playing on my part?

It's most likely the cab emulation you've chosen. Your hardware (DOD) may be the problem too...but I can't tell without hearing it. Your Audigy is fine....I've made killer recordings with an old Sh!tBlaster Gold 64 card as well as many cool recordings using my Realtek stock cards.
 
When something is harsh, it's usually in need of a low pass. Most guitar tones can be low passed all the way down to 4k if they are harsh sounding. But you have to experiment with how far to go down. 4k may be too far...you may be better low passing to 6k or 7k. Each tone is different, so never just do a starting point.
 
You mention specific "harsh areas". What makes you think they are harsh? Are you seeing them on a graph as spiking up? If so, that doesn't always indicate there is a problem there. Be careful with graphs. The greatest looking eq curves can be the most problematic while the ugliest curves can sometimes sound the best.
 
But if I were you, I'd try to get to the source of the harshness. This harshness...would could call it a "fizz" or sorts? High end abrasiveness perhaps? If so, it's going to be 1 of 4 things...or a little of all of them.
 
1. The cab emulation you picked: Some of these are loaded with fizz. I beta test for quite a few guitar plug companies and now own a Fractal Audio AxeFx II....which is the king of processors and cab/amp emulations. Cab emulations are intimate and personal...as scary as that may sound. But what I mean by that is, you need the right cab to compliment the amp as well as other things which I'll cover. But try a few other cabs and see if the harshness goes away.
 
2. Mic placement/the right mic: Amp sims give you choices on mics as well as where they can be placed. Some harshness can be dialed out just by moving the mic AWAY from the center of the cone....just like in real life if we were to mic a cab. Closer to the cone gives you more fizz/treble, further away takes the fizz/treble away. So check the mic as well as where it's placed to see if the harshness fades.
 
3. Your DOD: I can't really comment on whether or not the DOD may be contributing here, but you very well may be over-doing it. The only thing I'd use in that DOD going into Amplitube would be a light compressor to condition your sound. Any other distortion, eq, effects, speaker sim in the DOD etc, could really be problematic and degrade your sound. What happens when you remove the DOD and just try to get a tone out of Amplitube alone?
 
4. Your ears: As bats mentioned in his great advice, you need to know what a good tone is before you can build on it. Some guys (and I know this as a teacher of sound) feel treble replaces distortion, so they over-accentuate it. The reason being, they don't yet know that distortion/drive/sustain comes from lots of things that built your sound into an entity. One thing doesn't give you a good tone...there are several. If you don't know what good tone is, you can sit here and drive yourself crazy. So make sure you can identify with what good tone means. It will save you years worth of trial and error. Also watch effects usage. Sometimes they can add harshness in as well if you're not careful. In a nutshell, all of the above can cause the problems you've been dealing with.
 
Here's how you can start to learn a bit other than having someone literally teach you about tone...
 
There are multi-track versions of pro bands you may know and love scattered on the internet. Search for them. This will give you a general idea as to what one of your hero's sounds like without all the other instruments. The first thing you'll hear is, they use WAY less gain than you think.
 
Removing excess gain in your tone cleans up your sound in seconds and is a necessity. On the other hand, too much gain removal may not be right depending on what style of music you are after. So you'll need to research that.
 
So try searching for some multi-track versions on the net and load them up in Sonar or whatever you use. Listen closely to the tones and compare them to yours. It won't be a perfect fix for what you're going through now, but it sure does help to have a general idea as to what your sound is like when compared to their sound. Best of luck Fender, I hope some of this helps.
 
-Danny

Hey Danni, I am not sure if it is my DOD pedal, I have no effects going thru it, it's just set on a clean slate with max volume. I found the harsh points (or what I consider to be harsh) by setting my Q to 12.0, +15.0 DB then just moving around the frequency. I can hear the difference between smooth and harsh frequencies by doing this, for instance 4100 can sound smooth to me then 4200 starts to be ear piercing then 4300 can be unbearable, then moving thru to 4600 it can sound smooth again. Now, is this a good way to do it? That I don't know, but that's what I did.
 
I also just tested using a lowpass filter set to 7500 with a Q of 0.60 and it helped in the same way.