Why have you got your shares & downloads going into your program folder? If you update LW, then it will install over the top of & delete your shares. The default location is normally C:\Documents and Settings\"your account name"\Shared

Sharing folders, it doesn't really matter how you arrange because other people will only see a single list no matter what or how many folders you have them in. eg: If I browsed you with my LW, I would only see a single window without folders just like a normal search results.