I haven't switched to ISBoxer yet, but am really contemplating it.
From my understanding, if you enable the FTL options...
You can press a hotkey in any window, and the same key is broadcast to the others.
If for example the hotkey is 1, on the default action bar.
And you have Account 1 - Fireball, Account 2 - Shadow Bolt, and Account 3 - Lightning Bolt.
The two accounts which you are not on, will automatically target the same target as the target of the toon in the window your mouse is in (ie the active window).
You could change to either of the other windows, and they'd automatically target whatever the active window is targeting.