I’ll give it a go…
Yes.
A layer (this is where I get confused) holds zones. I can use a layer to house similar zones, ex. I have kick, snare, HH - 3 zones all on one layer.
Yep.
Or I can use layers to stack zones as velocity layers
.
This too.
OR should I consider each set a layer. Kick is layer 1, Snare layer 2, so on.
Could do, yes.
Whenever you need to be able to select, effect, or operate on a set of zones independently, then Layers are what you use to ‘group’ the zones together in order to do that, e.g. :-
Organising → quickly selecting sets of zones
Editing → adjusting the parameters of several zones together
Effecting > add effects to groups of zones
Playing → use modifiers to control which zones play.
Etc etc.
What exactly a layer contains is up to you, and will depend on what you want to do to, or how you want to treat those zones, how & where you use layers is not fixed in any way.
HTH.