I had a nice, long reply for you but I was just about to post it when the forum went down. Ah, well, lets see if I can't get it back.
First, nameplates are assigned via texture replacement, which in turn is accessed from the ship editor window in recent versions of FRED. Click the button, and replace the texture "nameplate" with the name of the nameplate file you've created.
Secondly, you have to create the nameplate file yourself outside of FRED.
Karajorma's Freespace FAQ has links to a good nameplate tutorial and the appropriate font, and is in general a good document for a new FREDDER/modder to have bookmarked as it contains a lot of useful stuff. The tutorial for making Orion nameplates is excellent for the Orion, but doesn't work for any other nameplate-enabled ship; those need transparent nameplates. The difference being, an Orion plate has a specific texture that the name is added to, whereas a transparent plate is white (usually semitransparent) text over a completely transparent background.
As for the tools you'll need, if you have access to photoshop then that will do nicely. If not, I recommend
The GIMP as it's free and quite powerful.