The sub you choose will determine the size the sheetrock cutout needs to be. Do you have a sub or will you be building one?
As long as the sub is flush with the opening it should work, I think?Ideally, you really don't want to do what you're suggesting. Any time you put a sub or any other speaker back in a recessed 'tunnel' like that, you're going to completely change the frequecy response and cause all kinds of resonances that you really don't want.
Bryan