first off wii64 will never run indiana jones and the infernal machine that is a n64 game that is extremely hard to emulate becuase it had an exclsuive done microcode and those factor 5 games are all a no go on most emulators you can check the compatibility here
https://wiki.gbatemp.net/wiki/Wii64_Compatibility_List
Second the games must be extracted, if you n64 games are in zip or rar you need to open them and get the roms out, they need to be files in z64/v64/n64
third the wii64 path is sd:wii64/roms/here
forth
nintendont doesnt detect the game becuase its probably bad naming/patch
for
nintendont to run games you need them to be iso and then you place the iso on
sd:games/anyname/game.iso
your iso needs to be called game.iso not just the last part need to be .iso, make sure your pc is not hidding extensions and you actualy end up renaming stuff game.iso.iso or have more folder in between the game and the games folder.