It works the same, from IS Boxer pressing it, as it does holding both keys at once without IS Boxer.

You just want to make sure the drop down box, beneath the hotkey selection window, is set to "on" for Hold Keystroke Actions while key is held. That way, you can hold Shift ~ (or whatever your hotkey is, for the formation you are doing), and the toons will continue to move in the defined directions, until you release the key.