I currently have a gigabyte 6800 ultra, is it ok to SLI that with say a BFG 6800 ultra or other brand?
and does it affect anything if the GPU on one is overclocked and not the other?
The latest drivers from NVidia allow cross over from maker to maker as long as the core is the same and it has the same number of pipelines. So yes two 6800 Ultra's from two different companies can be used in SLI.
I would suggest taking the OC off until you have SLI running then OC them together.