If you want to replace the old MS ships with new ships, follow this procedure. This way whenever a stock or downloaded mission calls for a stock ship, your new ship will show up instead.
Let's say you want to replace the stock MS "SHA_ESSEX_CV9" with one of Collins super detailed Essex class aircraft carriers. It's easy to do and the process will apply to any replacement ship you want to use in the place of a stock MS ship.
1. Rename your original MS ship to something like: SHA_Essex_CV9_Orig
2. Make a new folder in your ship folder and name it: SHA_ESSEX_CV9
3. Unzip Collin's Essex class and place the contents of his ship in this folder.
4. Rename the DP file from USS_Essex44 to: SHA_Essex_CV9
5. Open up the Ship.cfg file and edit in the following:
FROM:
[fltsim.0]
title=USS_Essex44
sim=USS_Essex44
model=
panel=
sound=
texture=
TO:
[fltsim.0]
title=SHA_Essex_CV9
sim=SHA_Essex_CV9
model=
panel=
sound=
texture=
Save and return to your main menu and now whenever you select a mission that calls for the stock MS Essex, your new Collin Shipyard Essex will appear.
Remember that the sim= line, the DP title and the ship's folder name must all match or CFS 2 will not be able to load the ship. Somehow they are interconnected and must match. Follow this procedure for any MS ship that you want to replace with a more detailed one.
I rarely see a stock MS ship anymore and when I do, I bomb it till it sinks!