This is assuming you are using Warcraft, which I know you're not.
But I don't have Star Wars, so cannot give you the exact information for that game.





Start up: IS Boxer Toolkit.

In the top left pane:
Left click on the + to the left of Key Maps.
You should see something like: Control + Combat + Non-Combat.

In the top left pane:
Left click on Combat.

In the bottom left pane:
Expand your Mapped Keys, by clicking the + (if it shows - Mapped Keys, and the list then it is already expanded).

If you left click on the first one...
You should see Hotkey: 1
One Step.

Clicking on the "1" under steps (lower left pane)...
In the lower right pane you get some information.
In Warcraft you have a mapped key for assisting the current window.
And then it sends "1" to all windows.
You can click on the Assist Me and the 1 > All, to see the commands.

You'll want to change the 1 > All, to be 1 > Current Window.
Do this by left clicking on the 1 > All, in the lower right pane.
And in the far right, you see Target, and in the drop down box Window: All w/ Current.
Change that to Window: Current.

What this does...
No matter what window you're in, when you press "1".
It sends "1" to the current window, and does nothing for the secondary window.

You will want to do the same, with each of the mapped keys that you use.
If something is not listed as a mapped key, then don't worry about it... as that is not broadcast to the second window and by default is current window only.

Once you're done that, you need to add mapped keys that will affect the second window only.
I'll assume you will be using "1", as one of your keys.
Even if you're not, it's probably easier to make a copy and edit it.
In the lower left window, Right click on DPS 1 (or whatever the first option is called).
Select Make Copy.
At the very bottom, we have just made "Copy of DPS 1".
Left click on this mapped key.
In the bottom right pane, it says Hotkey.
Left Click the Arrow to the right of your hotkey.
Press and hold Shift, and press the desired hotkey (Shift + 1).
You can repeat the process for any hot key you desire (Shift + J) or whatever.
Left Click on OK.
Left click on the "1", under Steps in the bottom left pane.
We need to edit the "1 > Self", so left click on that (in the bottom right pane).
Change the target from: Window: Current to Window: All w/o Current.
Repeat this process for each desired hot key.

Once done, File Menu > Export to Inner Space.




This gets you...

Push any key, and it affects the active screen only.
IE, whichever screen has focus.

And push the same hotkey (anything you configured for Shift + Hotkey) but with SHIFT held.
And the action is sent to the non-active window.