The traditional way is direct out to the recorder - it keeps operator error at the minimum and wiring the shortest.  However, with 8 outs and 6 ins it will be confusing anyway.  I would think 4 direct outs and the stereo signal (or alt if Mackie supports it) would give you a lot of flexibility.
 
@

Hi, AT. I certainly have a buttload of flexibility with this mixer (there are a ton of other possible output configs I didn't mention). I actually have a total of 8 direct outs (as well as mains, Alts, monitor, summed mono, hi quality stereo headphone AND the 6 Aux outs... there may be more I'm forgetting). It's a super nice board which I'm glad I picked up before I descended into extreme poverty.
 
If direct outs are the traditional way I'll be sure to keep that as my failsafe, especially when signal purity is needed. I'm going to try the aux method as well just to see if there is a noticeable difference because I really would like that extra level control before it hits the interface and Sonar (because there are no trim controls for those inputs on the Scarlett). Currently it'll be for crunchy guitar stuff so any noise introduced will probably be completely overpowered anyway. The signal is going to get split before the amp/mixer and one signal sent DI to the Scarlett Multi In anyway so there will be a pure signal available.
 
Really I'm just experimenting at the moment to see what I can get away with and what works the best. 
 
Cheers. I hope you've been well and thanks for the advice.

Bah. I kind of spaced on what you were saying. The confusion either way should be minimal now that I understand the board a little better. Aux and Alt and other strange outputs/inputs confused the heck out of me until today but it's all very simple in retrospect. All I'd have to do is stick to the numbers. Knob 1 = Aux 1 = Scarlett in 3, Knob 2 = Aux 2 = Scarlett in 4, etc.
 
What gets confusing is how Sonar sees the inputs what with the "In 1" and "In 2" on the interface both being called "In 1 (left, right and Stereo)" but I'm used to that now. No biggie.

I've got a 1604VLZ also, and used the 8 direct outs for my drums into my Delta 1010. I loved being able to control the individual toms after they were in Sonar. I used a couple 4 channel compressor/gates hooked up to the inserts to gate the drums as they were being recorded. I agree Beepster, it's a nice little board.

Hi, Leadfoot. They are pretty slick aren't they? Unfortunately I was a little too... er... uneducated to really make full use of it until now. I kept creating loops and doing other stupid stuff when trying to use it beyond basic i/o. It was very frustrating but after not touching it for a few years and learning more about audio it's making a heckuva a lot more sense.
 
Yours is a little more modern than mine. I recall seeing that model when I was looking at mixers but they were being sold for at least twice as much. Mine is the original version and it is pretty huge. It also, IIRC, doesn't have some of the extra features yours does that are more geared toward digital recording (but what those features are I have no idea at this point).
 
I really lucked out when I got this. It was something like $300 in mint condition whereas others around that price were beat to hell and none of them came with the additional input pod. Apparently it had been sitting in a hotel board room tucked away in the podium or something and only used for speeches and stuff. It might as well have been right out of the box.
 
I was testing it out a bit yesterday through Sonar and man does it sound good. The EQ is particularly nice and I just learned today that Mackie designed the EQ to control things more logically in regards to music (as opposed to usual band placement on older boards... or so they claim but it does seem to make a difference). I used to use it with my old Layla 3G and Nuendo but I think it sounds much crisper through the Scarlett and Sonar. It has been a very long time since I used the old set up though so I could just be imagining it.
 
Either way I'm glad I kept it as opposed to liquidating it during my great poverty purge a few years ago.
 
Cheers.

Man, you got a really great deal on it! How many tracks do you plan on recording at the same time? If it doesn't exceed the number of inputs on the Scarlett, I definitely vote for the direct outs as opposed to the auxes.

Well with all the wacky stuff I want to try and a desire to get as many possible signal sources (so I cab choose/blend the best) I could see using up all 8 inputs on the Scarlett (with the multi jacks) but for most stuff I'm thinking 2-4 off the board (like two for the Line 6 dual channel outs and two for mics on the cab). Then a split clean signal going DI via the multi jack for sims.
 
When I start recording acoustic guitar I might go crazier but I would need some more stands... lol.

Lol...I hear ya. I've heard one of your songs and love your playing, BTW.

Thanks, man. Just wish I had more time/energy to get more stuff produced. I guess that's a common complaint though.

I recently sold an old Ramsa console due to down sizing. I always used the direct outs to my Alesis HD24v XR.  It worked fantastic and left the aux outs for cue mixes and effects. I agree with Scook on the shorter signal chain of direct outs, less chances for routing and gain staging errors, etc. You may benefit from a patch bay to repatch mixer channels to your DAW as needed.
 
Rocky