If you're referring to 'pilotable' ships (ones you can 'drive') then they get installed to your \aircraft\ folder like any airplane. (They're basically a float aircraft that can't fly, only taxi.)
Once properly installed you select the ship from the 'Select aircraft' window just like an aircraft.

Most downloads will have install instructions in an included .txt file.

So it's ships ya want, eh, matey?  Well, shiver me timbers if it ain't yer lucky day.  Break out yer drool bucket, cauze they're out there, all ya gotta know is where ta look.

OK, enough of that.

Mitsuya Hamaguchi
 
An absolutely spectacular modeler.  For FSX and FS2004:
  > Titanic
  > Freedom of the Seas
  > Le France
  > Norway
  > Coast Guard Cutter.
  > Asuka
Others I've forgotten.

All with incredible detail. 

There may be some of these here.  But if the mods don't mind, if I may redirect you to where I got them:  Flightsim.com.  Just drop his name in the search engine there.

On SimV there is also the HMS Endeavor, a great sailing ship model that you can 3D on and actually walk around the deck.

But wait, the best is yet to come:

If you search this at Flightsim.com:

Cape Liberty Cruise Port

You will see two add-on scenery packages:
The Cape Liberty Cruise Port with the Freedom of the Seas docked and ready to move.

And the Queen Mary II scenery package, with the QM2 docked in Brooklyn, also ready to move.

They need some auxiliary scenery, also there and specified, but the installation is not difficult and well worth time spent.

And they do move.   Just install and follow the instructions, both ships can be animated either separately or together; they will disembark from their dockings, sail out through the Verrazano Narrows Bridge, turn around, and come back and dock.  Is that far out or whut?

And here's the real thrill of it all:  While they are sailing around, you can fly over them in the aircraft of your choice, or even take another boat out and sail around with them.

Enjoy!