Wow, that was unexpected! Thanks gibs for doing that, I know it must have taken quite a bit of your time.
ClassicWB does mix ECS/AGA in one directory, in fact all WHDLoad games go in one single directory (with letter drawers).
Demos go in another separate directory (but again all types of WHDLoad Demos).
As for the best method, Iím not sure. You could have two versions, but then thatís twice as much work when you want to update anything.
Or you could have one version that detects (or has an icon tool type setting) as you said.