I really don't get why you're hung up on this save stuff. Managers exist because there are different ways of running things (i.e. running Nintendont on a regular Wii through real gamecube memory cards). In this case you would want a save manager to copy data out of the memory cards. But this...
You don't have to use those things. Just focus on getting one thing to work at a time. You'll want to use save managers later if you want to backup individual save files or copy saves to your console.
Wii games will save to your WIi/vWii's memory, just the same as if you ran them from Disc. You don't have to worry about saving. NIntendont, whether it's run from USB Loader GX or standalone will also try to save in the normal way (using the gamecube memory cards).
However if you are using a...
SaveGameManagerGX allows copying Wii save files to/from USB/SD. GCMM is what godreborn is thinking about, which would indeed be useless on a WiiU or any Wii without Gamecube memory card ports. It's meant to manage Gamecube memory cards.
If you are emulating the memory cards with Nintendont...
You are probably missing files on your sd card or they have been placed in the wrong location. Are you able to share what your sd card directory looks like?
USB Loader GX can use cheats from a txt file and apply them to both Gamecube games and Wii games. Internally it will generate a GCT file from the cheats you've selected from the txt file.
USB Loader GX is my preferred way of running Nintendont so I'm not sure how cheats work when running...
An ISO is a copy of your game disc containing all of the original game files. A patched ISO is literally a modified copy of said disc, so the original files have been completely changed. There are methods to patch discs and replace files, but often an easier method exists (i.e. Riivolution for...
I will also point out that I recently softmodded a new wii and thought I could get away with a USB flash drive, but it lead to many black screens as you described. Eventually files started getting corrupted and I simply had to buy a new external hard drive. I'd recommend you get one before...