I also start with a main page, and this page will link to /root/ (with user/password) /list1/ , /list2/ (user/password) and /home/ (public access).
My main-page is a web-page without any filelist, but where you can logon. After I link directly to root or list1, list2 ...
I did it as follows: Take a stdtemplate, eliminate things like upload an filelist, put your page in the main section of the template and you can use the login-link an have also access to the hfs values like ip, username, users connected and so on.
Then put in root, list1,list2,home (in your case it may be homework,uploads,random ans storage) a diff template.
So you are logged in in the mainpage, and you don't have to login any more. (naturally, no user can access the '/' (vfs-root), because the template is your webpage.