For the key mapping question, there's a few things you can do. The easiest is probably to make a few different Key Maps, and start out with them unassigned. Use a Key Map Action to enable each one at the proper time. So, for example, maybe you have 3 Key Maps for this, and one of these Key Maps is assigned to your Character Set, making it the default. In each of these 3 Key Maps, you would have 1 Mapped Key for casting your spell, whichever spell needs to be cast depending on the Key Map (using the same Hotkey for each, but a different Key Combination for the WoW Macro Action). You would also add 1 or more Mapped Keys specifically for switching Key Maps, which would each have 2 Key Map Actions -- one to disable the already-active Key Map, and one to enable the one you want to switch to.

Repeater regions are per character. Until you hit the Sync button, the regions you configure in the current window are independent of the regions in the other window. So one thing you can do is set up the one most of them will use, hit Sync, then switch to the window you want to have a different one, and edit the regions there. Delete the existing region if you want, or hit the Clear button, then just add the new region that goes to the new targets.