I did not see an option to change the sub setting for stereo different than for direct.
You can however change the sub settings for multichannel sources differently from stereo sources. Also, you can change the sub settings differently for all of the various multichannel modes (widescreen, cinema, stadium, ect.) so you can have several settings pre-prgorammed.
MY sub definitely has the ability to blend in with the music, but for most of my music I do not feel I need a sub at all.
I was listening to some rap to test my sub, and This particular track was definitely VERY bass heavy.
The gain is at about 60% on my sub(where it was at during the audessey eq setup.
Audessy set my sub at about -12db, and I upped it to about -6.5db, so It probably is running a little 'hot'
I will adjust it down later if needed so the sub is more subtle, but I am just testing it's abilities right now
I have not had a chance to listen to my sub much with HT yet, been very busy.