duplicating duplicates

I gave to try and sort out the part of the site my brother has been working on. Gacktrek was his incarnation and he wanted it up along with up and coming projects as well as previous vids. – He is not a web designer and I have been trying to teach him how to do it all but it aint happening. The result is much duplication of files and folders. – I wanna tidy the whole thing up so its all nice and tidy!!!!