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I would suggest moving or getting rid of the retail client (if you don't actively play it) and putting the WotLK client in the default place. The reason I say this, is the default settings for World of Warcraft, under the "game" and "game profile" part of the setup wizard point to your program files/world of warcraft folder.
So this would (should) eliminate the need to add the game like I talk about in the second option..
OPTION 2: (only do this if option 1 will not be good for you as far as getting rid of retail)
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If your wow for warmane is located in another place (which it sounds like it is) you may need to close out your game, and create a new "game" with innerspace. You can do this by right clicking innerspace in the bottom right of your computer (the taskbar) and select add game. Then give it a name, like WoW wotlk or something and then for the executable, point it to where your wotlk is and the wow.exe
When you run the setup wizard with ISBoxer, you HAVE to make sure the correct game is selected.