Just because your speakers have "built-in subs" doesn't mean they are optimally positioned. Part of the magic of separating the subs from the mains is that it's pretty rare to find that one location is ideal for both. Likewise, not all subs are created equal, and it is certainly possible that the built-in subs don't go quite as low as you might like.
And, yeah, calibration is a good thing. Have you got a setup disk (like Avia or something)? An SPL meter? How do you have the subwoofer outputs from the receiver connected to the speakers? How high is the gain on the subs?
