Just make 2 folders, call them whatever you like. Put your console stuff in one and the other stuff in the other one.
Having your Launchbox on the root of your drive is just pointless, it serves no benefit and only causes issues.
Set your drive up like this
L-
- Launchbox1
- Launchbox2
- Games
- sub folders separated by each platform
- Emulators
- sub folders for each emulator