hey blackcom,
Personally I prefer to do them seperately, because you settings will need to change from tom to tom depending on the size and tone of each tom (obviously)
The best results I've had have been leaving the toms dry (no verb, or very little) and fairly heavy compression. About 4.1 ratio and slowish attack with about 6-10db of compression, it may seem a lot but it really helps to make them pop out of the mix.
I usually filter out quite a lot on the rack toms as well.
try some heavy compression with tasteful attack and release settings (accenting the skin sound, but still letting the whole hit get through) and panning them fairly wide)
as long as the panning doesn't overlap with guitars or pads, they should cut through quite well.
hope this helps.
-j