If you want to be SURE that your game is at the correct place, in the correct format, correctly named : Dump it yourself !
Put a gamecube disc (Orignal/backup/multi Iso) in the loader and select Dump feature.
You will see where it goes on the HDD and how it's named.
Then put your others games on the same place/folder layout.
Be sure to use the latest revision (not version) of the loaders.
Install DIOS MIOS 2.2 if you want USB loading, or DIOS MIOS Lite if you want SD loading.
In the loader, select the correct version of the installed MIOS, if the version you select manually in the loader doesn't match the real installed version, then it will load only the inserted game from disc, not the ISO.