Since the old city covers only 3 square miles and parking is limited, walking is often a good idea. Fort San Cristóbal has a small parking area from Luis Munoz Rivera Avenue after you pass by the Capitol.
Fort San Felipe del Morro does not have parking facilities and is a 1/4 mile walk from Bulevard del Valle street and El Morro road.
If arriving on a cruise ship, most piers are withing walking distance (10-15 minutes). Just walk up the hill, past the Plaza Colon. The Panamerican pier is 3 miles away and taxis are available.