If they came with any sort of .tbl or .tbm etc file, you could add them via a modular table. You would still need to add them to a mission of some sort. You could start by extracing a retail mission from the VPs, editing it in FRED to have the new ship as a player flyable craft, and then put that in the missions folder. So the minimum to use it would probably look something like:
-Freespace2
--newships (this is the mod for testing)
---data
----maps
-----textures here
----missions
-----edited missions that have the new ships
----models
-----any new ship models
----tables
-----a *-shp.tbm file for each new ship
Then you would select 'newships' as a mod in the launcher, and play the missions you edited. If you take retail missions and rename them you could play them in the mission simulator in the single missions area, and in fact that's probably a better idea than overriding the retail campaign missions.
If your ships did not come with a table, you'd have to come up with that yourself, or try and get some help from someone on the forums.