Upsample isn't directly associated with any particular sub trim - it is just a processing mode. If you use it with a two-channel source (which subsequently rules out any matrix surround processing, as upsample can't be combined with processing modes like that), the two-channel sub offset will be in use only because you're in a stereo mode. If you use upsample with a Dolby Digital or DTS 5.1 source (which also rules out matrix surround processing modes that would produce 6.1 or 7.1 from these 5.1 sources), the two-channel sub offset isn't applied because you're not in a stereo mode.

If you have too little bass in two-channel mode after configuring the system to work properly in multichannel, then there may be some other settings that need checking. First, I'd make sure (just to cover all the bases) that the tone controls are zero'd out - or just turn "tone defeat" on to bypass tone controls - so that there's no funny business going on with bass and treble controls. Next, I'd look at the material being used to evaluate bass response: make sure the multichannel source using to calibrate isn't somehow weak in the bass area, and that the two-channel source being used subsequently isn't too hot in the low end. After those two, I'd take a second look at my bass management settings - if the sub seems too strong in music playback, you may want to dial the front channel crossover down some. I had to do this with my SVS 25-31PCi in our old house, as any crossover higher than 40Hz made the sub way too noticeable with music playback. You might also check sub phase to see if reversing the phase works better.