to hopefully answer some of your questions:
The Pi completely runs off the SD card, which means once you exchange the card and put another one in it is as if the other card never existed. Nothing for you to uninstall.
To use RetroPie you have 2 options:
Either use the RetroPie-Setup script to install all necessary software components inside an existing Raspbian distribution (like you possibly have installed using your NOOBS card), or getting a preinstalled SD card image.
The latter might be the better option if you are looking for a ready to go solution. You just download the SD card image, write the contents to an SD card and you are ready to boot from it.
For this you can either use your existing card (replacing the NOOBS image) or get a new one. If you get a new one the size depends on the number and kind of roms you would like to store on the card. I use a 16GB card and this covers the roms I use on the system very well.
As for storing roms on an external USB device, I think it might be possible, the default rom paths point to a place on the SD card though and you would have to change them. I haven’t done this though, so this should probably be confirmed by someone who has…