Go to the maps section of Carbonite's options, and choose the one to adjust the minimap. Clear the box next to the first choice that combines the two minimaps" if that is what you prefer. The Blizzard minimap will show in it's usual place, and you'll be able to set up Carbonite's minimap independently of Blizzards.
Or,
You can right click on the combined minimaps and clear the box next to "Full Size".
However, if you like using both alternately as I do when I want to see if nodes are available where Carbonite says they spawn, then you may want to just decrease the size of Blizzard's minimap so you can see both all the time. After clearing the box next to "Full Size" as I suggest above, you can adjust the "docked scale" a couple of lines below the "Full Size" setting and move the slider to the right or left until the Blizzard minimap is small enough for you to see mostly Carbonite's minimap and Blizzard's minimap in whatever corner it shows up at by default.
To change other options to the minimap, just go to the "minimap options" the maps section of Carbonite's options and adjust it according to your taste.
I hope this helps.
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