You can technically do it, yes. It sounds like you might be trying to use a Keystroke Action to activate an ISBoxer Hotkey? (specifically, the slot activate hotkey) Keystroke Actions will never do that by design.
Instead, the Window Actions will let you do this. Window Focus Action will let you set any of the windows as your input focus (meaning that typing will go to that window) and if your Swap option was Always, that would be sufficient. However, since you've got your Swap option set to when you use a specific Hotkey, you're going to have to use Window State Actions to move the windows around.
So here's how to do this. Normally I would say to use only one Mapped Key and use it for all of your Click Bar buttons, but as it turns out the Window Focus Action doesn't support focusing the "current window", I'll have to correct that. That just makes this a little more complicated to set up... unless you enable "Focus follows mouse" (or manually focus the window after swapping with this method) instead of using a Window Focus Action.
For now let's leave out the Window Focus Action so I can keep this simple.
Set up a Mapped Key, 1 step, add 2 Window State Actions. First Window State Action set the Target to Window:Current, Where = Foreground. Second one set Target to Window:All w/o Current, Where = Background. Recommend leaving How set to Instantly, unless you don't use Instant Swap.
Now... because we picked the Targets based on "current window", this same Mapped Key can be used to move ANY window into the main region, by having that particular window execute this mapped key. That means you can have your Click Bar with 5 or however many buttons on it, have it do this Mapped Key, and set the Target for the click bar button's action .. to the window you want to activate (e.g. by Slot). So button 1 might say activate window -> 1, button 2 might say activate window -> 2, and so on.
Enjoy