wow, you are way ahead of me!
a little nomeclature first so we are using the same terms. a bulkhead fitting has three parts - body, gasket, and nut. some have two gaskets, i don't know why.
the body has a neck which is the part that extends through the opening in your pond. as you say, the neck has to be long enough to go through the opening and have enough threads left for the nut to tighten.
i put the neck through the gasket and shove the neck through the opening from the inside of the pond, then put the nut on the outside of the pond. that way the gasket is against the liner. i have always done it that way and it has worked so i assume it is correct. i have never used a lubricant or sealant with a bulkhead fitting, but i am sure there are many ways to do it for specific applications.