For WC2/A, copying the modified ships into the \GAMEDAT folder should be enough (note however that this will not affect the 'special loadout' versions of the ships - these are stored separately in a file called altships.dat (I think) ).
For WC4, I have no idea at all. I've never bothered editing that game.
For WCP/SO, it's a matter of placing the saved ships inside the \SHIPS folder (if necessary, create the folder). However, WCP by default checks the TRE files first - this means that you need to hack the relevant TRE file so the game does NOT find the ship there and instead checks the \SHIPS folder. All in all, you're much better off editing SO.