Typically the way it works is that the entire kit is recorded with a mic on each drum (going to a separate track) plus a pair over the whole kit, maybe another pair further out in the room, and probably a mic on the hi-hat. Every mic going to a separate recorded track. The signal from each drum track triggers the playback of a sample of that same kind of drum (only better-sounding, we hope). The overhead, room and hi-hat tracks are usually left alone, so what you hear is predominantly the samples, with a bit of the original drums from the overhead and room tracks mixed in.
The process is a lot closer to automatic than it used to be, but it can still involve a lot of editing and cleanup to deal with "false triggers" and such.
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