I had to delete my WTF, Cache, and Interface folders

[Svpernova09]

I need to mention also that when I run a single instance of the game I get a different UI than when I run an ISBoxer instance.

Example:

I run bartender and when I have a single instance running I get my bars in the special keyboard layout that I created.
In ISBoxer I get the generic blizzard setup and I have to reset all my bars. It did save though after I did it once so it is recognizing a wtf file just not the main wow one. This applies to recount, omen and the other addons I run.

WoW.exe when run by itself (not via ISBoxer) will *always* write the last configuration to WoWFolder\WTF\Config.WTF when you exit the client. Each ISBoxer window will write out their unique .WTF files defined by the file names in the characters.

Is it possible for me to run to instances of wow manually then have ISBoxer reposition and control them?

No.