I agree that SD3 is a good place to start.
If you then want a different program, then I strongly recommend EZDrummer - sounds fantastic, lots of usable MIDI grooves, easy to use, expandable and can crossgrade to Superior at a later date.
Not sure about other MIDI controllers,but the Roland ones (I have the A300 pro) have velocity responsive pads for programming beats.
As to using the pads on the Boss, do they respond to velocity? It's vital if you want your parts to sound natural.
I'm sure I've seen a video of one of the Cake staff do some pretty good, intricate sounding "Real drummer" parts using the step sequencer, so don't dismiss it out of hand like some of the posters. I don't use it myself, but if I remember where the video is I'll post it.