Using FLB oder TLB on more Computers

Of course, those files you refer to above are in different User folders under documents and settings. Do I need to make these links manually for the second user?

Generally YES. But TLB can fetch files from ALL USERS and Current User profile for these folders only:
ADMINTOOLS,
FAVORITES,
STARTMENU,
PROGRAMS,
STARTUP

If you create Virtual Folder linked to the All Users then TLB fetch files from current user profile too.

Also you can add a Desktop Virtual Folder. It will show files for all users correctly.