hello i am building a custom system and fiberglassing a woofer enclosure and rear deck for 6X 9's

i was wondering about my ports, there supposed to be 4" wide and 8.35" long each. I want to run the ports though the rear deck and fiberglass them in beside the 6X9 speakers. Now does my port have to be flush with the sub box, or can it stick out of the box? will then length change if i do that.?? can this setup be accomplished?