Two parts to this answer. The first is how to best enter the notes because, as you alluded to, they're nearly impossible to enter manually (talking purely MIDI here).
I first bought the SPD-20 (in the top middle) to do this but it probably had the same issues that the Korg Nanopad does. So it turned into my "effects" (MORE COWBELL!) and I bought a starter V-Drum set. It wasn't long before I had maxed it out to what you see above (damn was it fun!).
Next, I was using the DR 808 extra that came with one of the early versions of Cakewalk for the drum sequencing because you could map a sample to a MIDI note which meant I could change out samples all over the place (I had a bunch). The other feature I liked about the DR 808 was that you could have multiple samples at different (Ai! Lost the correct word! Dammit...) volumes/levels/strengths (hope you know what I mean!).
Anyway, I don't know what the best replacement is for the DR 808 now, but that's the basic idea! It's kind of fun to make a complex fill and then look at what it creates in MIDI - you can definitely see that doing it manually is not going to happen!