It depends on how many drums you're layering (two or three is typical), but the trick is to divide it up by frequency band. This is one way of doing it for kick drums, for example:
Sub - Heavy bass tone (think 808 kick)
Mid - The "smack", no low bass content
Transient - The "snap", short and clicky, no bass content at all
This is how a lot of modern kick drums are made from what I understand (e.g.
this is how the Vengeance guys do it, and it's what their Metrum synth does). The only difference here is that you're starting with fully finished drum samples instead of custom made pieces.
The trick is to pick out a drum to use for each frequency band, and then completely EQ out all the frequencies that you don't need for that band. Try to pick hits that are strong in one specific range of frequencies and use them for that band (i.e. don't pick a top-heavy kick for the sub layer), so you can EQ them as little as possible and retain as much power as you can. When EQing, you want to make sure that there's very little overlap between the hits because they'll build up mud. This is especially true in the bass range, where the low tones can phase-cancel and sound horrible (this can completely destroy a kick). You also want to remove the attack from every layer except the transient, to further reduce overlap mud.
Practice at it a while and it'll start making more sense, hope this helps
