There are graphics provided in these folders as an example of what the system expects when these graphics are loaded in. Each type of tileset has a subfolder in these, and graphics files of single tile blocks go in each. Inside there is an AceRTP and MVRTP folder. The Custom MV and Custom VX Ace settings load off of custom tiles folders, found in the directory with the Tileset Builder application. The tileset builder is usable without configuring any of these folders, but you will be limited to the Custom MV and Custom VX Ace folders. When selecting a folder, you need to select the base folder for that maker, and not any folders inside it.
The Folder Manager is used to set up the RPG Maker folders. Black background when removing tiles from a tileset loaded in that was saved without transparency.