Got it straightened out. I'm leaving this information here for folks that come here after me.
1. Don't download or try to upgrade SoaSE Trinity via GameStop. It will not work.
2. Contact the developer Stardock.
3. Register your game with them.
4. Download the latest version or patches.
5. Pull out the individual games i.e. if you want to play SoaSE "vanilla" create a shortcut for that game.
6. Download the individual trainer for THAT portion of Trinity and you should be good to go.
Hope this helps.
Worfster
Thanks for simplifying all of it Worfster, and thanks to CH staff for the trainer.