Open your inventory, on the bottom there should be a tab called "catalog", if not, your version of starmade does not support blueprints and thus there isn't a sure way to port the ships.
If it does support blueprints, enter your ship(s) and create a new entry in the catalog for each one. Once finished, move the blueprints folder within your StarMade folder into the StarMade-folder of the new install, or just update the old installation to the latest version. The blueprints remain and you can spawn them in from the catalog tab again.