If you made the ships with the in-game designer there are only two files that make up a ship: an .xml and a .shipcfg file. They can both be found where the save games etc. are stored, the default is AFAIK C:\Documents and Settings\[your user name]\My Documents\My Games\GalCiv2\ships (and of course this is also the place where people using your ships need to extract them to). You will recognize your ship files by their file names.
Make sure that you include the right .shipcfg files. Note that the game attaches a number to them and they get saved under a different file name every time you save the ship during the design process. To find out the right .shipcfg file you can either look into the .xml file (there is only one per ship name) or choose a new ship name before you submit it to the library (so that there's only one .shipcfg with that name either). Name them anything you want since there is no commonly accepted naming convention right now for ships.
It's a good idea to post ships that consist of hull and jewelry only so that people can use them as templates. I suggest including the following information in a readme.txt and/or the submission text:
-required GalCiv2 version
-if Collector's Edition stuff is needed
-other stuff required (e. g. Kryo's Hull System Mod)
-which race(s) can use them
-any technology requirements apart from the hull class
-installation instructions
-anything else that might help
You have to submit a .zip with all your files in it and a 200x200 pixel .jpg preview picture for the library. They should get accepted as long as they don't infringe copyrights.
Hope this helps