You don’t have to programme your beats in separate tracks. There are no rules. Do it your way, make tracks however gets you a pleasing result and change shit up when you are ready. You can always programme with everything in one track if that’s what you are comfortable with and copy paste the individual hits to separate tracks at a later date. If you decide you need to.
It’s not ideal, but you can set up separate tracks that just send CC to control automation only. These are separate tracks to the ones containing the notes that are triggering your sounds.
So you have notes in your programmed drum track (as per your current set up) but CCs in another that will mute say, you kick drum whilst the mute track is active and then unmute the kick when the track is inactive.
But this “mute over CC” workaround will only work if whatever you play your drums from has per voice or per sample volume control with either it’s own CC number or the ability to assign a CC number to a parameter. So look in your midi implementation chart for whatever module you use and see if the kick drum has a volume CC number of its own.
If they do, you could probably even assign CCs to the assignable performance knobs and use them to bring hits in and out of the mix whist you trigger tracks from the pads.
Have to ask, what do you play your drums off?