I separate everything out to different tracks (kick, snare, hi hats, exc).
Because while it may sound great on its own or in small mixes, when you begin to add 15-20 tracks of Bass, Vocals, Guitars and so on...these other instruments rob frequency's. thus the kick must be dialed in properly.
EZ drummer is a great Drum sim but there is no possible way to dial in a great authentic sounding kick by merely using the EZ Drummer interface.
By splitting up the kick it also allows you to sound stack drums a lot easier. for example using drum replacer to add a few more kick samples. I have found the best kick and snare sounds are those that have multiple samples combined and not just one track. by having a main kick and then layering it with 2 more samples it really thickens things up nicely.
Also keep in mind the only way to use real good plug ins like waves, exc to dial in the perfect kick sound is to split the kit up so each instrument is on its own track. In order to hi pass / low pass certain kit pieces to clean them up they have to be on separate tracks.
At all cost when ever possible use a real kit. I don't care how great the samples are, it will never, ever beat a real kit.
But if you don't have a real kit at your disposal and your trying to fudge a real drum sound, separate the kit pieces.
Here's the best way to do it with session drummer 3