Boomy bass is the trickiest thing to calibrate properly in your system. Here are my recommendations that often times help:
Using your receiver's test tone and an SPL meter, adjust the sub volume so that it's in-line with the rest of your speakers.
Position the sub as far away from corners as possible. The closer to a corner, the boomier the bass.
Try experimenting with the crossover setting. Usually there's two places to fiddle with this: the receiver and the sub. On the sub I generally say leave it around 80. But you'll notice that as you adjust it up or down, it will change the tone of the sub. Usually turning it down will tighten the bass a bit. On the receiver's crossover setting, I have found that the bass gets substantially punchier when set at 100, vs the usually recommend 80, at least in my room. I think the sub might do a better job tightening up the 100 Hz range better than the bookshelf LR's.
Sub Cable upgrade. It's true that an inferior sub cable can make the sub sound boomier and more sloppy than it should.
Receiver upgrade. If you don't have a receiver that gives you crossover adjustment, might be time for an upgrade. An important note: Some receivers have built in bass boost that you can't control - it's hard wired into the receiver. From my experience so far, Harman Kardon and Denon seem to be the most neutral in that regard.
Give the sub some time. Usually after 100 or so hours of use, it starts to loosen up and become more fluid = tighter more accurate bass.
If you want to get serious with your calibration, you can use a test disc like Avia or digital video essentials, and an SPL meter.