Yes, of course. Just drag and drop the navy on any city with a port. Better if it's a big city so it has enough supplies for the sailors. Copenhague is the most obvious place.
Stil, if you play with hardened attrition option all units will suffer some attrition (sickness, deserters...) even if it's a fleet on port or a garrison on a city.
The fleet has limited use for what i've seen, so i will not spend much (if any at all) on replacements for the ships.