Trying to get into this practice.. How do you guys do it? Is your amp setup in a different room? If it's in the same room, then how can properly hear sound coming out of the DAW to make sure that is the sound you want? Doesn't your amp sound interfere with the sound coming out of the amp? Any advice for a beginner in this area will be helpful...

Putting the guitar speaker in a different room is one way.

Another is to use an amp that sounds good at low volume. Even better a very low ampage guitar amplifier (under 2 watts if cranked) and an inefficient speaker then use headphones for monitoring the amp and DAW. I wouldn't be surprised if more recordings have been made with the old Fender Champs (or the local equivalent) with volume set about half way than bigger amplifiers, even if only for the sake of everyone's hearing. Being in a room with big amp or two hammering away for days at a time gets very wearing very quickly.

A third is to use a speaker simulator designed to replace the speaker and present the right load to the amp, such as the Palmer ones (valve amplifiers always need a correct load connected to the speaker outputs or expensive sparks and blue smoke are likely).

A fourth is a low power amp (again) and a speaker plus microphone in an isolation box.

Here are a couple of good resources. There's a bit of humor in the video. Just saying.
 
http://www.soundonsound.com/sos/aug07/articles/guitaramprecording.htm
 
http://www.seymourduncan.com/tonefiend/recording/how-to-mic-an-amppart-1-the-basics/
 

 
I have a Fender Rumble 200 v3 with a built-in DI. I record both the DI and amp. I use a Sennheiser e 609 Guitar Mic to mic the speaker.
 
http://en-us.sennheiser.com/e-609-silver
 
What I love about that mic is its front-facing design. I drape the mic over the cabinet and get it to hang right where I want it. I have no problem hearing the amp through my monitoring headphones. 
 

I have a kinda hybrid set up here at home.  The guitar amp goes in a small "sun room" (old porch glassed in) which comes off the main studio.  But there is no real isolation - you can hear the guitar amp in the main room.  W/ the band I'm working with the guitarist and bassist (DI'ed) are in the main room along with the singer.  She gets to do a scratch vocal and usually they don't even need headphones.  It captures the feel fine.  You can do the same thing w/ a big enough closet for the guitar amp.  For a while before I got the sun room we would put the singer in the hall and all use headphones. 
 
Recording in the mixing room does make it hard to be sure you are getting quality sound.  Usually it is a matter of setting the mic a few times and working out the best place to put everything in the space.  Then it is variations of that set up.  I use a cheap (-$100 ribbon) on the guitar amp and know where to place it.  You can also record tests until you get a feel for how it sounds best.  The less problems your room has, the more you can back off with a mic, like a ribbon.
 
 

I just tried a few things a couple weeks ago and they worked for me. My room is large (23'x15'x10') with all hard surfaces, so I faced the amp diagonally to minimize early reflections. I was originally going to toy with mic placement, but found centered between the speakers allowed for the direct path signal to overpower reflections fairly readily. I used a cheap diaphragm condenser (MXL V63M) at about 24" from the amp face and about 8" off the floor. Dead center was also chosen to minimize phasing issues, since the floor is hard and this is a 2x12 amp. Monitoring was done via headphones to prevent feedback into the mic. As the amp was set loud enough to outshine all else, the input gain could be set low enough to eliminate a lot of background noise from the takes (I was actually surprised by this, since this mic is not one I would recommend, and has always given me grief to pick up everything).
 
I am not sure what your setup is, but making sure the direct path signal is dominant (do not "square-off" to a wall in the front or rear), being aware of mic placement for potential phasing issues, and using headphones (if within "range" of the mic) will be a good start. There is no cook-book answer for this unfortunately as a lot is dependent on your environment/setup, so do not hesitate to try things to see how they work for you.

i use a combination of various mics,
and this:
 
http://www.palmer-germany.com/mi/en/PDI-09-Passive-DI-Box-for-Guitars-PDI09.htm
 

I use a Palmer DI box. Very useful things. I've used it for gigs as well if the amp needs to be in the PA. Unless you need to be pushing speakers into distortion, which takes a lot of volume, it's no worse than a carefully set up mic and far better than a mic set up in a hurry or positioned with a view to minimising crosstalk rather than optimising the guitar sound.

magik570
Trying to get into this practice.. How do you guys do it? Is your amp setup in a different room? If it's in the same room, then how can properly hear sound coming out of the DAW to make sure that is the sound you want? Doesn't your amp sound interfere with the sound coming out of the amp? Any advice for a beginner in this area will be helpful...

Monitor what Sonar is recording via headphones.
 
This will also give you the opportunity to experiment with mic placement  - the phones will attenuate a bit of the dry signal from your amp unless you're playing at insanely high levels, in which case a separate room would be required.
 
When close mic'ing, Sonar will record exactly what the microphone hears which is totally different to the sound YOU hear in the room.

I love my ribbon, but usually use a dynamic too. Sm57

I'll just throw in a couple of alternative ideas. Instead of mic'ing, you could take a direct feed from the amplifier's preamp out or effect send (if it has this). Then, after the part has been recorded, you could play it back routed through the amp and use a mic to record some room ambience.