It's not exclusive to ISBoxer but you can definitely set up hotkeys that send keypresses to specific game windows. What you've described is perfectly viable, if you find that comfortable and suiting your needs.

The fun part is that it's very much all down to preference. There's a near endless way of how you could choose to set things up and try to handle different aspects of gameplay. Finding what works for you and fiddling with the setup to get the most out of your team and being able to handle what the game throws at you is a large part of the experience for a lot of us.