What exactly is the problem? My custom folder is "Steam\steamapps\common\Counter-Strike Source\cstrike\custom". If you want to install VPK mods, than you can just copy-paste them into the custom folder, but if you want to install unpacked mods (models,materials,sounds etc folders) then you have to create a directory inside custom and then paste these folders inside. For example if you download a skin which isn't packed, you would copy the materials/models/etc folders inside "cstrike\custom\pink fluffy unicorn\"
1) Go into the custom folder. 2) Create a new folder, name it anything you want. 3) Drag and drop the 'materials', 'Models', 'sounds' and any other folders of the mod to the newly created folder. 4) Ya done. its installed.