That has been talked about before among the community. I think it is safe to say that once interiors are released and all the major bugs are worked out Cryptic will start releasing missions for it.
Ideally, each ship interior piece would have a reference point for mission-related content. So if the engineering deck gets boarded by Klingons or something, then because these generic reference points would exist in all map pieces on the Engineering deck, no matter how they are customized, it would still work.
In terms of bridges and so forth, each of the consoles that are there would have a designation, like science, engineering, tactical or command. By default, these would have a null function, but missions might designate that a player use a command console or a tactical console, and the hook for it would already be in place.