The Bose "bass module" (not really a subwoofer) is designed to be used with Bose gear. You already mentioned the speaker connections are on the sub. Also, I believe the internal cross overs are in the bass module and are set to work with the cubes (i.e., not a typical cross over frequency.) Finally, the bass out of those things is lacking (of course, that's just my opinion) So instead of trying to make it work my recommedation is to save up and then buy a good, decent priced subwoofer. This will enhance your home theater experience.

Here are some suggestions:
Hsu Rearch:
Axiom Audio:
Onix Rockets: