you can do either, but the size / length of the reflex tunnel needs to be adjusted. that's what sets the resonance frequency together with the effective volume of your enclosure.
I've done speakers with ports being part of the wood work and others with tubes, the later being easier to adjust. you should not trust the calculators blindly, as the volume is sometimes difficult to calculate.
as a special 'gift' from the physics department - the smaller the enclosure, the longer the required reflex port for a given frequency. going to a smaller diameter helps a bit, but gives you other issues.
cheers,
Michael