have you tried the provided settings yet? Once you find something you like, just a slight tweak to your taste, that's all it takes.
But since you asked:
I set my tone like this: bass: 9, mid: 12, treble:1 and leave pretty much leave it alone.
master: 2 to 3. As high as you can tolerate the floor (hiss) noise.
I adjust the presence depends on the pickup. 10 for strat/tele type, 12 for PAF or P90 type.
Adjust the gain to taste and also depends on the pickups.
See, it starts with what guitar/pickup you have.
Also try the speaker impedance plug, for some reason, I find the mis-matched setting to be pucnhy and snappier