With regards to box volume should the number I enter include the port volume as well?
No. Simply just type at "Volume" the useful volume into Vb, the tuning frequency into Fb, and at "Box" the displacement value (speaker's displacement + bracing, etc, but port's no) into Displacement. The designer counts out the port's displacenet, and automatically add all displacements to the box.
If you roll down at "Box", you can see there is Useful volume, and Total volume. Useful volume will be the same like the Vb, and Total volume is the real volume of the box, so Useful volume + port's displacement + all other displacements.