I highly doubt the rxv-757 can store separate speaker distance, speaker size, and xover settings for each input - most receivers of that class cannot. The settings are global and apply to all inputs.
Matrix surround modes like PLII Music/Movie/Game will use the subwoofer.
I'm not familiar with that receiver, but some have settings that allow you to choose the preferred decoder for any particular format you play. If yours has that capability, you could set PLII Music as the preferred decoder for 2 channel signals and tweak the parameters for the sound you like. If you set a different decoder for other formats, like DD, that would at least partially accomplish your goal because you would only use PLII Music for 2 channel signals.
I use PLII Music for everything. It is the most flexible of the decoders because you can set Center Width, Dimension, and Panorama. If the center sounds a bit weak on CDs, change the Center Width to a lower number which emphasises the center a bit (less gets sent to the front speakers). If the sound seems too far forward or backwards, change the Dimension paramater to move the soundfield forward or backwards. Panorama wraps some of the front channel signal into the surrounds, thus slighly emphasizing the surrounds.