Port length, through a decklid

Thank you in advance for anybody helping me out with this one. Ok this might be a very elementary question but im really needing to do this properly the first time through so please bare with here. The vehicle i am working with is a 02 Lexus IS300... i recently ripped out my Diamond Audio / Kicker setup because it was really kind of a temp setup with only a single 10" sub ported through the ski pass in the rear seat. This time around i will be doing a 3 sub configuration and im currently shopping subs. The Rockford Stage 3's, JL 10W6V2's, and the Eclipse SW7000's all in a 10" were catching my eye. But i am very open and would like to hear feedback on those who might have had experiences with them or any other sub that might be in this range or slightly better for performance. Ok to my real question since the IS300 is a trunk vehicle and it actually has a piece of metal between the seats and the trunk i wanted to port the subs into the deck lid to bring them more into the cabin of the vehicle. Now after calculations of port lengths and diameters, is the length that is called for for each application the length of the port that runs "inside" the box or is it the "total" length of the port as if lets say my setup called for a 4" Dia with a 10" length but i had 4" between where the top of my box meets the deck lid. Would i A. make a total 10" port and have only 6" of it inside the actual enclosure and the extra 4" running up to the deck lid? Or would i B. make a 14" port so that i have 10" in the actual enclosure and then the 4" to the top of the deck lid? Im sorry for the detailed and looong question but i figured i should be as detailed as possible.

Thanks for the information. Looks like ill be taking a different approach with this whole trunk now. And this is why i came and asked here simply looking for an answer like that... to correct my improper way of thinking.