The simplest way to replace the stock models with custom ones is to rename the folder, the .mod, and the brk.mod to the same name as one of the original models and just swap it out.
Example: Take your favorite Fed CA (Connie or later era). Rename the folder fca and rename the model files fca.mod and fca_brk.mod. Then just swap out the stock fca folder with your custom one. The directory for the model folders, assuming stock install location, is C:\Program Files\Taldren Software INC\Starfleet Command Orion Pirates\Assets\Models. Inside there you'll find all of the model's folders. Replace the entire folder, fca in this example. The custom model will require it's own texture maps, etc.
Sorry if I'm giving you info that you already know. I'm just trying to be as complete as possible, not insult your intellegence. If you need a walk through we can IM, if you like. When I first started I had to watch Chris Jones' "ShipEdit video tutorial" about 100 times (Well, maybe 99).

Ooops! You asked about EAW. It's the same except for the directory where the models are.
C:\Program Files\Taldren\Starfleet Command II\Assets\Models