Alright, first of all, turn the level down. You need to get the balance right, and it sounds like you don't. I had this sensation like the bass was coming from another room, and it was because of two things -- I had a whole...erm...hole in the frequencies between the sub and the bookshelf speakers, plus I had the level too high. If you have (or can create) a CD with a frequency sweep, it'll help (perhaps Troy can generate one? Probably complete overkill with Garageband, but who knows...?). Turn the crossover down until you hear the bass fade out, and then fade back in. This means that your crossover is now set too low, but don't turn it up yet. Get the levels right, so that they sound like they're about the same at their peaks. Then turn your crossover up until the gap is gone.

That's for starters. Now, listen to some music with which you are familiar, and adjust to taste.

A good sub actually makes you want to turn the bass down, surprisingly enough. I thought when I got my first set of full-frequency speakers (which had built-in powered subs), that I'd want to turn it up. Turning it up is just a compensation for the missing lowest frequencies. Once you have them, you don't need to turn them up any more.