I took no extra steps. I put the files where they were needed to be and ran it no problem. Many games don't work, and there's no pattern to it. For example, I was able to get Pokemon Stadium booting once, but never again on that exact ROM.despite doing nothing at all differently.
For now, it really just is trial and error. Several of my games boot, but it took some different ROM versions to get that far.
Also: If you're not using a NEW Nintendo 3DS/2DS, I'd assume the program is MUCH more buggier as on my O3DS tests, several games wouldn't boot unlike the New3DS counterpart.
As for how I'm running the emulator, I'm loading it through the Homebrew Menu using the HBL installed to my Home Menu as a .cia