An Audyssey/SVS sub controller or Velodyne SMS-1 sub controller is the easiest way that I know of to integrate a sub seamlessly. These devices also add digital room correction in the bass region which is IMHO a fantastic benefit. They're not inexpensive - the fully automated Audyssey/SVS is about $800 IIRC, while the Velo SMS (which still takes some work to achieve best results) is about half that price.
Good Luck
Marty
Good Luck
Marty