Okay, first, you need to either update the main shaders to include these effects, or delete them altogether (thus causing the engine to fall back onto the built-in default shaders). Second would be to enable them using post_processing.tbl (or delete the existing one to use the built-in default), see this
Now, to use these effects in a mission, the following things need to be done:
(I am assuming for the purposes of this tutorial that you have a mission where a shadow ship decloaks, strikes, and cloaks again).
1. Place the shadow ship. Open the ships editor, and mark the "Cloaked" checkbox in the Misc dialogue.
2. Open the events editor. Create an event using the ship-effect sexp, and select "Decloak" as the effect, with a duration of your liking.
3. To cloak a ship again, use the ship-effect sexp once more, only this time using the "Cloak" effect.