alright so you're trying to REPLACE portions of the SD kit with other samples, using aptrigga, by triggering audio with it.
this isn't the best way to do this, because aptrigga works beautifully with MIDI and and takes some getting used to when triggering it with audio.
i do the same thing, but with a different approach. here's what i recommend you do:
1. start off with just superior, and your MIDI. nothing else.
2. make a new empty track for each drum you want to be triggering with aptrigga.
3. make sure snap is on (alt+s) and ctrl+click the MIDI to duplicate it on each of the new tracks
4. now say you have a new track you want to trigger a different snare sample with. open the MIDI on that track, zoom out, and delete all of the hits except the snare hits. this is really easy..just zoom all the way out, identify the snare hits, delete everything above and everything below.
5. do this again for the other drums.
6. the end result should be a separate track with its own MIDI, just for that drum.
7. put one instance of aptrigga on each track and load the appropriate samples
8. the MIDI, instead of audio, will trigger the samples with exact precision and will void any fear of incosistency caused by the audio of superior. it will also save a little CPU load, as there's no triggering algorithms going on.
ESPECIALLY IMPORTANT IN REAPER: make sure ALL the MIDI feeding the aptrigga instances does not have any velocity 127 hits. 126 must be the max, due to an obscure bug.
now... if you're using slate, and you wanna take it a step further....
say you have your MIDI snare track feeding aptrigga. duplicate it a few times, and put all those duplicates under one folder called "slateSnare" or whatever.
use each instance for a specific velocity level. example:
slateSnareFolder
---slateSnareCrack
---slateSnareHard
---slateSnareMed
---slateSnareSoft
---slateSnareRoll
So you have a separate aptrigga instance with those particular samples per velocity layer loaded in, and then you just snip the original snare MIDI file and plop the pieces where they belong corresponding to how hard you want it to be. this, if you're using slate, is the best way to do it if you want full control over the velocities. ....atleast this is how i do it and it works great.
Make sure each instance of aptrigga is set to RANDOM when doing it this way.
now if you don't want to blend the samples with superior (which i think is awesome), you can just go into the superior construction window and disable whichever drum you don't want. this will save you a bunch of RAM, too.