RVLoader runs entirely off the USB drive. Once it's installed, you're meant to discontinue usage of the SD card slot. All your games, Virtual Console wads, and homebrew apps should be on the USB drive in order for RVLoader to properly detect them.
Ignore anything that any tutorials you've seen have told you, RVLoader doesn't work like other loaders.
The Wii games can be titled whatever you like, so long as they are in wbfs format, are placed within the "wbfs" folder on the USB drive, and have been split to suit the FAT32 filesystem that RVLoader requires. The filenames that are set by the isotowbfs tool are fine. Wii games can also all be in the same folder, they don't need to be in individual folders like Gamecube games do, but you can put each game in subfolder if you want to.
Gamecube games must all be named "game.iso" and be in their own named folder within the "games" folder on the USB drive. The only time a game should be named anything other than "game.iso" is if it's the second disc in a multi-disc game, in which case the file should be named "disc2.iso". You do not need to process the iso files in any way for them to be bootable, but you can "trim" the files to remove the junk padding data that fills every game to be exactly 1.36GB. This saves space on the drive, but is not a necessary step.
If you have named your Gamecube iso files correctly and they aren't showing up, you may need to enable visible file extensions in the Windows folder and file settings to check what the true file name is.