Ok, well that is weird, my husband also uses carbonite, and he doesn't get that overlap effect. We have checked that all our settings are the same but i still get the Blizz map underneath.
the point being I don't want to see the Blizz minimap at all, because I do prefer the zoom capabilities of the Carbonite map, and also as the Blizz map turns with the way my toon faces, and the carbonite is stationary, yes it does look very weird indeed, and also very annoying.
Infact all my friends who use the addon, don't get the overlapping when the maps are merged, just me.