Through the configuration option (right click on the IS icon in the system tray), you can change the default path to whatever you want.

I would suggest one wow install, with the configuration pointing to the install you want to run wow from.
Then get rid of the others, as symlinks don't provide any advantage over virtual files.
You can copy the Saved Variables for accounts and/or characters to the one wow you are keeping, to retain the settings you had for each toon.

If you really want to run multiple wow folders, you can "add a game" to IS Boxer.
Each game added will be warcraft, but don't go with the default profile (that will be one of your folders).
Instead have each folder be its own profile.

Honestly, I'd merge the folders into a single folder.
And run IS Boxer from the one executable.
And create virtual files for each toon inside the IS Boxer Toolkit.