2. I do not want the other toon to follow the alt unless the alt is in the main window. Would using the /click option help (where it asks to proceed normally or act like WoW not IS. I think there is 3 options.
I'm not really sure what you're saying, but here's what I think it sounds like you're looking for...

If you dont want ISBoxer to set the Jamba master and/or strobing when you switch windows, you can disable that and set a hotkey to do it manually. You can set a Hotkey for the mapped keys under Control, specifically the ones that say JambaMaster and Strobing. Then whichever character you want them to follow, switch to that window and hit the hotkey. You would disable the functionality when switching windows per Slot in your Character Set.