Depending on the thickness of the driver... You could do it a few ways, buth using a router or something simmilar...
1. On your baffle where the sub goes, use a router to cut a hole, then Rabbit a second hole around the 1st for the driver lip to sit in thus making it flush... However, you are making the baffle a lot thinner by doing it this way..
2. Cut a hole in the baffle like normal, mount the sub, then add a second baffle peice on top of that with a hole cut out for the woofer itself to fit though, making it look flush...
Hops those makes sense...