It doesn't matter what version of Carbonite the OP is using. If you do not tell Carbonite to NOT merge the maps, the maps will be merged and you won't see the Blizzard minimap unless you look at Carbonites minimized map while pressing the "ctrl" button which will make the Blizzard Minimap visible in the Carbonite minimized map.
You can separate the maps by opening Carbonites options (type "/carb options" in chat, right click the Carbonite minimap button and choose "Options" in the menu, right click a non-icon area of any Carbonite map and choose "Options" in the menu) to the "Map Minimap" page and UNchecking the "Move Minimap into Carbonite map (reload required)" option. It's the first one on the page so you can't miss it. UNchecking (or checking if it is disabled) this option will immediately open a "Reload UI?" confirmation box. Press the "Reload" button and the maps will be separated (or merged if they were separate before and you chose to check the box) after your UI reloads.