Lack of bass can sometimes be due to having the mains out of phase with the sub. Try flipping the phase switch on the sub.

The other thing you might want to try, is to play some material that has some bass in it. Turn off the amp channels to the mains. Make sure that you are getting any sub output at all.

Yamaha crosses over at 90 Hz. You could try the 950 at 80 Hz and 100 Hz to see if that makes any difference too.