It's not a problem, as long as you haven't tweaked any of the color controls there (and of course there's no reason to do that). And even so ColorNavigator never touches the video card anyway, it's all USB directly to the 16 bit monitor LUT.
I have a CG246 and an AMD card at default installation, so I assume CCC is in there. Never had any problems with that. It used to be that you could choose to install "driver only", but that's no longer possible. Now you have to manually deselect each and every component you don't want.