I use both Carbonite and Mapster(for dungens...) and they run really well together.
I don't have the minmap in carbonite though (maybe you do?).
I have Carbonite as a minimap (another addon I made removes the normal minimap and makes the dots a hud) and when I press "M" it opens Carbonite as a main map filling the screen aswell.
Then I have used the keybinding R_ALT+M to open the original map (it's in the carbonite section of the keybinding window).
Now if I press M it opens carbonite full screen and if I press R_ALT+M it opens Mapster...
Hope that works for you?
Regards,
Zas