They also have subfolders too, but those are dependent on what you want to do.
Personally, I make a folder that has backup textures and a set of new textures, which look like this: Since you have VTFEDIT, that means your textures and files are going to look like these: This part isn’t really necessary, but it always helps to have a backup of some sort for your files. (OPTIONAL) Setting up file format (OPTIONAL)