It's all personal preference. I used to sit pretty low, with my drums up a bit high on me, but since watching Mike Johnston play, I've changed it up and probably have my seat twice as high as it once was, with my drums a bit lower, so now I'm more on top of the kit.
Most people say that when you sit down your leg, from your hip to your knee should be parallel to the ground, and a 90 degree angle with your lower leg extending to the bass drum pedal. Mike says you can get more power and speed having your leg at a higher angle.
I think my bass drum playing is improving, but I'm not necessarily sure if it's because I've got a better practice routine now, or because I'm up higher, probably a bit of both.
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My Gear:
Yamaha
Sabian
Remo
Vic Firth