Hey you could have just asked me - PM is fine.
Gaticus was working the Wry Bash team to develop a better system for multiple game instances to access the same BAIN folder but read it differently with regard to what is installed per game instance. But then he disappeared.
So I've been getting by with multiple BAIN folders - one for each install basically.
This can be done by first activating a clone then going into the MOPY folder in the Oblivion folder and looking for the bash_default.ini - copy and rename it to bash.ini (if there is not a bash.ini already). edit that ini and look for the line that says sOblivionMods=..\Oblivion Mods (this is the default setting). Change each of the clones bash.ini to a different setting from the other clones.
So here are a few of mine:
sOblivionMods=I:\Games\BAIN Archives\Oblivion Main Mods
sOblivionMods=I:\Games\BAIN Archives\Oblivion Alt Mods
sOblivionMods=I:\Games\BAIN Archives\Nehrim Mods
Doing this takes up much more disc space (cheap these days) but does allow you to have BAIN active for each install and in a way that they do not interfere with each other. The downside is that updates that are used in both setups take twice as long to update. That actually is a drag, but hey - multiple games.
Gaticus - come back
Ok, I'm using a rather basic mundane setup (name wise) at the moment. I have Oblivion (base install) and 2 clones so I guess mine should look like so:
sOblivionMods=C:\Bethesda Softworks\Oblivion Mods
sOblivionMods=C:\Bethesda Softworks\Oblivion Mods_Ob Clone 1
sOblivionMods=C:\Bethesda Softworks\Oblivion Mods_Ob Clone 2
I am assuming your subfolders, BAIN Archives, are so they are just not under the same main folder your games are in.
I appreciate the answers greatly.