This is the folder structure:

./crosshairs/          Crosshairs
./env/                 Skyboxes
./gfx/                 Console backgrounds
./lits/                Colored lighting files (i.e. ".lit" files)
./maps/                Custom maps
./progs/               Models
./skins/               Player skins
./sound/               Sounds
./textures/            Map textures
./textures/bmodels/    Healthbox and ammobox textures
./textures/charsets/   Console characters
./textures/levelshots/ Level screenshots (loading screen while loading a map)
./textures/models/     Model textures (e.g. weapons, armors, projectiles)
./textures/wad/        HUD textures (e.g. armor icons, health icons, big numbers)

If a folder doesn't exist, simply create it.