So I'll pull the signal to channels 1 and 2 and record those. I'm wondering about fading though – should the channels be centred or panned left and right, respectively? My guess is centered given that the incoming right and left channels end up on their own recorded track, but I'd liek to be sure.
I would record the ISO (isolated) tracks of ch 1 and ch 2, and NOT bother with the "mix track."
(in firmware 9.02 go to second page of home menu, to the Record menu, and the top left box gives control over Rec L,R, turn it off, or off + linked is fine too)
1 will be left, 2 will be right, it should give you stereo WAV files at your desired rate & depth.
As to record levels, if you can find the max level and make it come in just below -0.0 dB (digital full scale) that will be great.
You can leave a couple dB unused if you like, but I'd have peaks higher than -12dB.
In fact if it's not peaking occasionally above -6 dB, then you are not utilizing the final available bit of the recorder.
I figure once you're using that bit, you might as well use it a lot!
If you are talking about actual AVERAGE levels, trying to gauge those from meters which read peaks might be tricky.