I have already tried direct mode and it didn't make any difference. I did turn my sub off and switched the LFE/bass settings between the Front and sub setting and I did notice more bass from the speakers when it was set to front speakers only.
I also double checked all the wiring last night and everything looked good. Even if something was reversed I think YPAO will detect it.
Its been so long since I heard how my old Onkyo sounded with music and although I wasn't getting tons of bass with the Onkyo I believe it was still a bit more than what I'm getting now. Of course that could be from the way two receivers sound and maybe the Yamaha is a little weaker in bass.
I used both my Onkyo and Yamaha for movies 95% of the time and both sound great. I wasn't too concerned with how it sounded with music until now because I mostly used my computer for music. So maybe its possible that maybe my JBL speakers just aren't capable of putting out good bass? Even if low frequency cancellation was the problem shouldn't I still hear lots more bass just by moving up closer to the speakers or another spot in the room? I already experimented with this and I do notice depending on where I am in the room I do get more bass but it still feels like its lacking a bit depending on the music.
I also spent all day yesterday experimenting with my sub and different locations and I believe I found a good spot for it. It seems to sound better with the crossover at 60Hz and it seems to blend it with the main speakers pretty good I think. I think I'm happy with the way music sounds with the sub right now.
Just for fun I made a frequency response graph using an audio test dvd I got from another forum and my Radio Shack meter. I'm not sure if I did it right but I basically just played the test tones and recorded what the meter measured. I played test tones from 25Hz to 120Hz. Anything below 30Hz is very low and my meter doesn't go low enough to detect it. This was done using just the two front speakers with the sub off and my LFE/bass setting set to front speakers only.