Yep, always use the final volume that the subs will see. After doing a lot of designs you get a good idea of how much volume a port is going to take up. So you just take the final volume you want, add on top the expected displacement of everything else(port/subs/bracing), and then work to get some dimensions that'll be right around that gross volume. Then you can do little adjustments to the port area/tuning to get port displacement right around where you want it(sometimes you may need to just alter the dimensions to get what you want with the port size/tuning)...maybe use some 45's to take up space inside the chamber, if you need to.