There is no easy answer. Even with e-drum pads and mic'd cymbals you still pick up the "click" of the stick hitting the pad (although this sound gets buried in the mix).
Even the use of noise gates won't solve the problem, since you need the gate to allow the decay of the cymbals - which almost assures that some other drum sounds will slip through.
You can stuff the drums with foam or other material to eliminate as much resonance as possible and you can muffle the hell out of the batter head to the point that when you hit the drum all you get is the attack of the stick with no real tone - but this will effect the drum response both to your technique and to the trigger (although this may not be a bad thing as far as trigger response - since it eliminates all the vibrations, etc. that can cause trigger problems).
If you don't want to go that route, you should try to tune the drums as close as possible to the e-drum tone you are useing, so any drum bleed does not "clash" with the e-drum sounds. The down side is any tuning adjustments also effects the triggers.
You would need to experiment with mic placement to get the least amount of drum bleed as possible. Hopfully the cymbals can be kept low enough in the mix (if you listen to recordings the cymbals tend to be a "subtle" accent) so that the accoustic drum sounds won't dominate the e-drum sounds.
Bottom line (at least in my experiance) is you can't stop the drum bleed into the cymbal mics, you can only work with it.
