I'm not sure how it's handled using the Coda rules but in Star Trek, I have often seen crewmembers figuring out alien ship controls w/o the benefit of understanding the alien language. It seems that knowledgeable & experienced crewmembers, esp. engineers, just have a knack for figuring out alien tech.

I suppose there might be some differences but I guess the theory is that ship controls are basically the same in most alien vessels, at least in the Alpha Quadrant. It may take some time to figure them out but it can be done.

I would say let them use their skills but add penalties for using the alien ship controls, at least until they've had some experience w/ it.