First, open up your Window Layout for editing by selecting it in the top left pane (under Window Layouts).
The main option you're looking for is the drop-down box that'll be at the top of the bottom right pane, "Swap Hot Character to main region ______". Right now, it's set to "always, for game windows". The "always" bit means that it includes when you Alt+Tab or click on a window, or pretty well any method you can find to switch to the window. If you don't want them to move when you click on the window, then you're going to need to pick an option from this drop-down box that does not start with "always". If you would like it to only swap when you press Ctrl+Alt+1, Ctrl+Alt+2, or whatever other per-Slot Hotkeys you configure, set this drop-down box to "only when I press a Slot activate hotkey".
After changing that setting to not include "always", the "Focus game windows via mouse without clicking (Focus follows mouse)
" check box unlocks. Check that box to make sure that when you mouse over to the other window, that you don't have to click on it to activate the window before doing anything in it.
Finally, one last thing to note, neither Slot in your Character Set is actually configured with
a Hotkey (note that in older versions of ISBoxer, that was normal behavior, but with the current version if you use the Quick Setup Wizard, the default hotkeys will actually show up in the box). So if you configure the above, and Ctrl+Alt+1 and Ctrl+Alt+2 do not swap windows, then configure them as Hotkeys in the Switching tab of each Slot in your Character Set. To do so, select your Character Set in the top left pane, then select each Slot number in the bottom left pane (1, 2) and configure the Hotkey box in the bottom right pane. The default switching keys DO use the "... make this hotkey global" option.
That should be it. Export to Inner Space and re-launch.