Neogamma works only with WBFS partition.
USBLoaderGX doesn't support loading .wbfs games from SD.
Other Loaders should support FAT32 SD card for .wbfs files.
I never tried SD loading, so I don't know which option you have to change, but I guess in cfg, you set it in the configurator or there's an option to specify which device you want to list (USB or SD).
Take a look at all the settings.