It depends what your way of playing with the changed files is I guess.
If you've edited the romfs, you should have your paragon output folder with the modified files.
One way is to rebuild the cia, and then install it to your 3ds or run it via citra.
Another way (and a much more convenient imo) to "enable game patching" with luma, put the modified files onto your sd card and then simply run the game. Luma loads your modified files then instead of the files it usually loads. The patching method also works with Citra. There's a mod framework where you can put the files into to have them loaded instead of the vanilla files.