I was thinking that if I could just tell the 2nd or 3 windows depending on how many someone is running that if they could be instructed to just back up but yet keep stay on assist of main that it would make playing it on the fly much easier.
To do this, you would make a Mapped Key, with the Hold option enabled, that presses your "back" key (e.g. S if using wasd) on whichever windows you like. You can definitely do that.
The idea would to be simply apply it to a key that the movement only goes to the 2nd window. Is that possible with IS?
Yes. You can direct your keystrokes to any Target, which may be any one or more characters.
Also to setup follow after the fight, using Keymapper?
Yes. If the game provides a way to hit a key to auto-follow, you can set up a Mapped Key through ISBoxer to send it (which configures KeyMapper as you mention).