Well, you need something on the bottom to stop the silica from running out with your solvent. I usually use columns with sintered glass (see picture) at the base. A plug of glass wool does the trick as well [I would put a thin layer of sand on the cotton as well - to prevent clogging/blocking]. I don't know about cotton wool.
I think it's a good idea to get someone to show you how to do it for the first time. After several columns you will develop your own technique. It is quite a popular technique, there is a lot of info on the web.