You can download limewire to a shared folder Like C:\Documents and settings\All Users\Documents. Then install it from there on two seperate accounts. Then you will both have your own version running on your own account with seperate folders for your files.
If you both try to run LW at the same time LW will automaticaly choose a different listening port for the one that was started last and you could have some trouble with your firewall if you haven't allowed access for the other port.
Or you could run the one version and manually move the files to seperate folders.
Hope this helped