Make a hole in the case, where the port aims and keep the sub's port as close as possible. Stick it if you can. You will create quite some air flow inside the case, which should keep things cool.
Nah, I'm just kidding.
Subs should be magnetically shielded, I don't think you'll have a problem with that. But all those vibrations inside the case might damage something over time.
Best placement for a sub is in a corner, with the speaker aiming the wall or floor. The air port should also aim towards a close by wall, 5-10" or so. I guarantee a 200W will shake and rattle the whole room when placed like that.