So I have followed this guide: https://gbatemp.net/threads/tutorial-installing-rxtools-custom-firmware-3ds-and-2ds.390867/
Basically I have everything set up so that I can play GBA Virtual Console games. Now my final issue is not being able to use the red Gateway card with the .3ds files stored on it. Now the RXtools emunand is completely formatted over my old gateway nand as I understand it. So the old GWemunand no longer exists. Can I just use a different SD card for gateway, or it more complicated than that?
All CFW (Gateway, rxTools, ReiNand, CakesFW, etc) use the same Emunand. If you have homebrew, you can just download the Gateway package and use their .3dsx to boot into GWEmunand, and that would boot into the same Emunand that rxTools uses.