K I don't know if you'll like this setup but I can tell you how I do it:
First up make sure they didn't merge your standard minimap into the carbonite minimap. That's in options > map minimap > first checkbox (Move minimap into carbonite map). The reasons I don't like to have them merged is that the carbonite map doesn't show class and sometimes it's handy to know who is following you, and you cannot to the best of my knowledge ping the carbonite map for fc locations and such. Then again I have a lot of room so I don't mind having 2 maps visible.
Then right click the carbonite minimap and set the fadeout transparency to 0.40, and put it in a place you're comfortable with ( I usually use a long rectangle in the bottom right corner of my screen ).
For the map options themselves right click on the carbonite map > show > (uncheck) show punks, the red dots are the location of the person who last detected a punk and it's very misleading and inaccurate. You'll also notice there is a little checkbox on the first set of options that says [Follow You]. Next time you are in a battleground wait until the battle starts and uncheck this box after you have the map positioned to be centered. If you do this the map will automatically stop following you after the start of a bg, so which is good because if you don't uncheck follow it constantly moves so that you can't see the whole map.
The map is scaleable, so you can make it any size you want, and zoomable, so that when you're looking for the efc you can literally zoom in and see that they are actually standing ON the cap point in their fr. To zoom hold your cursor over the map and scroll wheel, to move what the map is showing grab and drag.
The result on my UI looks like this :
It's not transparent right now because I'm mousing over to check someone's hp but you see how it works. I always scale it to the standard shape of a WSG map. It's very helpful tho because I can with a glance see where my teammates are and what state their hp is in, which then tells me where I should run with the flag (for ex: 2 teammates just went from full to 0 in about 2 secs = stay away!) You can also see the carbonite flag carrier tabs at the top
As for your map disappearing, you can make it reappear by clicking the carbonite tab on the minimap up top or by hitting your default map keybind twice (first will show fullsize map, second will reposition minimap). You could also be seeing what happens when the map doesn't zoom in on your location; since the battlegrounds and dungeons are not part of the world it can sometimes take a while for the carbonite map to place you (and it never gets it for some dungeons). If you're seeing blank make sure the follow box is checked and move around a bit, then zoom to make sure you're not on it but just zoomed out too far to see.
Hope that helps! The setup sounds complicated but I promise the result is worth it

I feel blind when I don't have this thing.