If I understand correctly, you have a threaded pipe, two nuts and a rubber gasket? Further in assembling, in the inside of the tank, you have the pipe, rubber gasket and nut and on the outside, a nut?
If this is correct then couple of questions for you. How are you able to tighten the nut on the inside without creasing the gasket?
Based on what you are describing, I do not think you have what we call a bulkhead fitting but a double end threaded piece of pipe with two nuts and a washer. If this is the case, what I would suggest is:
A) see if you can acquire proper bulkhead fittings
B) if you cannot, then you need a flat nylon washer that will fit over the rubber gasket on the inside of the tank so you can properly seal the opening.