@bmulligan
The image includes Raspbian, thats the OS. Then the RetroPie scripts are on top of that.
But yes, there isnt an X window system pre-installed on the image.
I'm not sure why they arent showing up for you, unless its a permission related issue.
Are they all accessible by user pi?
Did you follow these steps exactly?
https://github.com/RetroPie/RetroPie-Setu
From your previous comment. If I where to accidently change permissions how would I go about fixing it? My problem is my emulators aren't showing up. All my files are in order but I have noticed my /home/pi/.emulationstation/es_systems.cfg
does not update automatically when I install a new package I have to do it manually. It worked for nds but can't seem to get it to work for snes. But I do remember accidently messing with permissions before hand at some point.