I separate the layers in at least three different frequency ranges.
I have an 808 for the sub bass with a low pass, an acoustic drum sample that's typically a meld between the bottom end and the top end;because it adds to the bottom and to the top, and then i hi pass a physical drum model (reasons kong drum designer) and make sure i can get the click to sit right by itself.
I typically route all of those different layers into different layers with the corresponding EQ settings for each. I also do a mix of the different layers according to taste.
I then record those sample going off and make it into one file. Then i add a transient shaper and boost the attack a bit and adjust the decay.
A note worth mentioning here, I adjust the attack and decay settings so that my 808 is the first layer to actually develop. Reason behind that is because, bass takes longer to develop than the other layers.
The middle layer has slightly more attack and less decay than the bottom layer.
The physical model layer, i cannot adjust the attack, so i leave it be. And good thing too, because i want it for the beater sound (aka your click), more so than a drum sound. And don't forget to pitch your drums before you record. It's best to have them oscillating well together.
But when you combine it, it should be pretty awesome. And when you get a solid recording, you can adjust the entire pitch to fit the song and adjust the attack with a transient shaper.
But, at first you want to just focus on the drum sounds rather than treating it to the song at first. Later you can go back and adjust stuff.
This technique also works for snares as i take a similar approach, but with slightly different settings due to the frequency differences (i also add in a side stick as well if the song is mostly a snare bias)
