I don't know what you're looking for, but combining the maps doesn't do anything to the "functionality" of Carbonite. It is designed to work that way. That's the way it works best.
You want to
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B - Remove the wow minimap and keep the buttons so I can use Carbonite completely.
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What buttons? The minimap buttons? Carbonite has it's own "Minimap Button Window" that takes the minimap buttons off of the minimap. It woks with or without the maps merged. So, what buttons?
The Quest Watch buttons? They are a part of the Quest Watch, so if you're using that the buttons are there.
If the maps are not merged you won't get the active node icon on the Carbonite map, but I don't know if there is anything else you won't get on Carbonite's map.