I'm using Cool Edit Pro. It does what recording/editing software should, except for real time effects.
The soundcard's a Wave 8/24, so no problems there.
I'm recording mono tracks.
Mixer Main Outs to soundcard Ins 1 and 2. Soundcard Outs 1 and 2 to mixer Ins 1 and 2. Mics 1 and 2 to mixer Ins 1 and 2.
When I tried two mono tracks, I noticed something strange. Cool Edit Pro has a recording level meter which indicates two levels. If I use two mics using the mixer inserts (or just straight into the soundcard through preamps), the level of each mic is indicated on the level meter separately - one jittering red bar for mic 1 and the other jittering red bar for mic 2. But when I used the mixer Main Outs instead of the inserts, the Level Meter bars fluctuated together, in sync - the level meter was either averaging the two signals (unlikely) or responding to just one input. So I decided to work with just one mic. Anyway, whatever mixer EQ I assigned it played back just fine from the computer hard disk. But no matter what panning I gave it, it only came through the headphones, and didn't get recorded to hard disk.
Okay pg, I guess you asked for it, but I apologize for all this boring description nevertheless. Welcome to the nerdolarium. I don't see how anybody else is going to benefit from this boring post.

Feel free to shake your head in incomprehension and walk away from this one. That's how I feel.