If Roxas had a strong sense of self and didn't seem to be losing it, he and Sora would work something out, just out of necessity. Roxas might find or make a quiet, set-aside place in Sora's head where he could curl up and give Sora some privacy (he'd probably do that anyway, really, so he could have time to himself too). He might also just kind of hover in the back and 'go along for the ride' sometimes, though I'm iffy on how Sora would feel about that. Taking control is something he'd probably have to get Sora's explicit permission on, though, and Sora would probably give it only on the condition that he be allowed to give warning.

... That said, Roxas taking over in an intimate situation would be a really, really interesting fic to read. I kind of want someone with more talent than me to write that, now. o.o