Then what exactly makes you think you have an emuNAND? That is very uncommon these days and you should probably consider switching back to sysNAND. There are instructions for doing so at
https://3ds.guide.
You should run your GBA games via open_agb_firm. You won't be able to launch them from your Home menu, but that's the best way.
Not sure you can install TWiLight Menu with an emuNAND. You can definitely use a flashcart.