AndrewS,

Yes, upsample will upsample the L/R channels.

I calibrated my 990 from the DVD input first with PL2X. Then, I put a CD in the DVD player and switched the 990 to Upsample and used the 2-channel offset to knock the sub down a few dB as I like my movie bass a little heavier than 2-channel.

When I had dual SVS subs in my configuration. I sent the signal to both of them simultaneously and then used the SPL meter to adjust the combined level of the subs to 75dB. The way I understand you are doing it is going to set them way too hot. If one is at 75db and the other is a 75+6 (81db) and they are combined you will end up with about 85dB (10dB higher than all your other channels. Also, it is important to remeber that the Radio Shack SPL meter (I assume this is what you are using) is not very accurate at low frequencies and is normally on the low side of the lower frequencies. All this (if I am understanding your setup correctly) meaning your subs are set way too hot.

I am under the belief (from my own experimentation) that the PL2 setting will be the same loudness (subwise) when you switch to stereo mode. To tone down the sub in stereo mode, you can use the 2-channel offset as it is the only thing that will affect the sub level in 2-channel mode after it has originally set in PL2 mode. This is definately how it is working in my system, beyond that I am not sure what your issue is.

Regards!