My 'System' setup for using my Shure FP24 out in front of the MixPre-3 for two channel recording:
System: Mode Basic
Line IN XLR
CH1 knob: Pan L, Input Line, Gain 10 (turn knob to the right)
CH2 knob: Pan R, Input Line, Gain 10 (turn knob to the right)
CH3 knob: Gain 0 (turn knob all the way to the left, for Off)
This will leave you with one 2 channel file, 24-48
Major EDIT: Previous setup, whether in Advanced or Custom mode, leaves you with multi channels in a single Poly file. This new setup avoids that.