I have already PMed Three_Pryme, but just to clarify for future readers: the ship editor now saves ships to the Particle Fleet's ship directory by default. That means when you click the "Save As" button and save your ship, you don't need to do anything else and you ship will be visible in Particle Fleet.
However use caution, since you can easily override an existing ship with no (or rather, limited) way to undo that.