Settings for WOW are in the Config.WTF file (from what I can recall anway). ISBoxer will create separate copies of this for each character if you have select WOW as the game when you configured the characters in the Quick Setup Wizard. If you created the characters manually, then you should run the Virtual File Wizard, select WOW and then add all the characters which do not have the 3 WOW virtual files.

The Virtual Files that are created (the per character copies) should then be used to save the individual character settings, so you can have different settings per character. The redirection all happens behind the scenes.

This also saves you from having multiple installations of WOW, which does nothing but chew up disk space, and prevents Windows from optimizing memory usage when you run the games. Multiple game installs should be avoided (sometimes you just can't, but where you can, avoid it).