a pretty obvious feature that people don't seem to use is the mute screen. when i master my finished sequences I'll often use the technique flux mentioned (which is sadly true, a lot of people DON'T use that trick and end up consistently muting the, for example, Kick and Snare from a track simultaneously. this gives some finished pieces a kind of jagged "dropping out" sound), and when i'm putting a sequence on my multi-track I usually do live mutes.
if you have a method to your madness, and isolate your drums and other samples on individual tracks consistently from song to song, you'll develop better communication with your mpc. you can save a template with renamed tracks to help you keep organized. i.e., save a blank sequence and rename the first 8 tracks to drum sounds you often employ: kick, snare, o-hat, c-hat, rimshot, etc... then everytime you make a track, load up the empty sequence to start and save it under a different name when you're done laying your samples.
once muting tracks with the pads live, you'll get a feel, like pad 1 is always your kick drum. you apply this to all your songs and you'll start muting them all in the same fashion.
this all may sound elementary, but until I learned tricks like these I don't think i was "playing" the mpc as an instrument.