I would suggest you to experiment and find it out yourself.
My guess is when you disable crossfire then only you see two devices and you can feed them individually with kernels. In crossfire mode they should behave as a single device but still computations should be possible on all the compute units. So my guess would be it should not matter atleast hugely.
Can you share your results as i am more or less guessing? MAy be some one else can give a better answer.
This link might also be helpful:http://forums.amd.com/devforum/messageview.cfm?catid=390&threadid=142700&highlight_key=y&keyword1=mrbpix