When you add a mapped key, it has a target.
In Warcraft (and it would likely be very similar in Star Wars), Window: Current is your active character.
And Window: Others w/ Current, refers to your other windows.
Anything you push, which is not a hotkey for a mapped key, will go to the current window only.
So for the most part, you're good as is.
Take advantage of the "Add Many Mapped Keys" function in the IS Boxer Toolkit.
You would want whatever keybinds you would like to be broadcast.
With a modifier of Shift + Whatever key.
And to send that keystroke (without the Shift) to the other window.
If you plan to always lead with Slot 1, you could assign the Shift + Whatever hotkey, to broadcast that hotkey to Slot 2 only.
If you plan on leading with either window, choose the "Others Without Current" as the target.
Once you're done, File Menu > Export to Inner Space.
Connect With Us