I just found out that I had a few "New Character slots" available, so I decided to put myself through the whole "starting out process", all over again!
Anyway, the character I created, has brought Captain Taggart's ship home", to Spacedock. Reported to Adm. Quinn, who directly 'commissioned', into Starfleet, as a Lieutenant, and ordered to assume command of the 'late' Captain Taggart's ship.
Now, it's at this point, that things start going "around the bowl, & down the hole" The character, is 'ordered' to immediately report to the Spacedock's shipyard to oversee the ship's 'refit' and provision, to be re-deployed in the fleet.
Now here's the thing. When the new Lieutenant is in the shipyard, (s)he, is 'granted' the ability to 'remake' the ship in their desired fashion.
Just how many times can you do this?
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Like @coldnapalm said, if you see a zen charge it's because the current set of choices includes something unlocked with a purchase. For ships that means buying another ship, for costumes it means either buying the costume unlock or sometimes buying a theme pack like the Bajoran bundle.
Always check that the cost is 0 before finishing a change in the ship and costume tailors.