If you're using my setup (Masterpack) I have separate icons and folders for GB, GBC and GBA which was working fine last time I checked.
As for the cover folders I don't have any covers so can't check if this works though it should.
However, not long time ago I started switching source menu spots when new plugins were out so now I have VBAGx icon for all GB's Gambatte for GB/GBC and GBA retro.
All the plugin inis are still there for GB standalone and GBC standalone, so all you need is to use the corresponding magic numbers and bring them back to your source menu.
Thank you so much. I got it to work. God bless you .
One other question, is there a way to change the default CoverFlow? So when I pick a Source it automatically displays like a carousel and not a big wall? (By coverflow I mean the thing you can change by pressing 1 or 2 on the WiiMote).