Wow i think your post wins an award for most vague!!
Sounds like you probably have the sub either in a bad spot of the room, have the phase set wrong or are just expecting more than that sub can handle.
First, please give us more info.
Room size?
Is it open to other areas?
Are your speakers set to small or large? If small, what x-over?
What are the speaker/sub trim settings in the Yamaha?
This will get us started in helping you. Try flipping the Phase on the sub. If that doesnt help the switch it back.
Have you ran YPAO?
If you can, go get an SPL Meter from RadioShack. This will help you in so many ways.
Read up on doing a "Bass Crawl" on youtube. You pretty much place your sub in your main seat then crawl around the room listening to bass heavy music or bass tones. You listen for the area in your room where the bass sounds powerful yet articulate. The you set your sub in the spot you heard it sounding good then you run YPAO & fine tune with the SPL meter.
Doing that should get you close to where things should be. You may have the sub in a spot that gives you bad bass response where you sit. Its not until you start experimenting with location, settings & EQ that you'll know if the Velo is good enough for your tastes.
Also make sure your speakers are set to Small & the crossover between 60-120hz. The x-over # should be set by ear. Whichever sounds best to you.
But give us some more info so we can help you out more!!
