Sub + BFD: Calibrate in Pro Logic or Stereo? (1 Viewer)

I'm getting ready to equalize my sub again since I've made some room changes. Now, I know most people recommend setting all speakers to small and let the sub handle all the lows, but after several trial runs with small/large/sub on/sub off settings, I find that the best sound (to me) is setting center and rears to 'small', setting fronts to 'large', and setting sub to 'on'. I use the excel sheet found on http://www.snapbug.ws/bfd.htm and the sine wave test tones to get a frequency response curve.

It has been stated several times on this board to equalize the sub with the front speakers on, and I plan on doing just that. The test tones are burned onto a cd. This means that since the source is NOT 5.1, I must put the sound mode in either Pro Logic or stereo. The $20,000 question is this: Should I equalize the sub while my pre/pro is in Pro Logic mode or in stereo mode, both of which utilize the sub? There are considerable volume differences between the two modes. I do not know if the relative volume between the sub and mains changes between modes, so I was hoping some people have some insight with this.

Thanks!

I prefer to EQ while I'm running on stereo, then cross-over the PL, PL2 or any other mode to ensure the bass is still smooth.

I find that the relative sub volume can change with respect to the surround mode I change, but the bass response should still remain relatively flat. Volume diff aside, the properly BFD should still maintain the relatively flat response in any surround mode.

The main reason I cal to stereo is that I can be certain the bass response and volume remains correct while listening to 2-stereo music which I'm slightly more critical of.

That should work just fine because on my initial measurements my room response didn't have any bad nulls.

Thanks for the input!