The cupping is an issue you should deal with before gluing the top on. It needs to be flat on the side that will get bonded to the body. Attach some full sandpaper sheets to a flat surface and sand it down level. I think ScottR has some pictures of this process in one of his build threads. Be prepared to use a lot of elbow grease using this method. Actually Scott can probably chime in here as he's done many of his tops around existing necks to cover his deep neck tenons.
As far as the F-holes, You'll usually want to cut them after you've completed your carve but before you glue the top.
BTW Are you using the oak for sentimental reasons?