I was manually updating a RF600VPN to (3.11). I used the WinSCP to copy the files to /home/loginuser, then I SSH into the box, but when I try to move the files to /var/spool/autoupdate I get a message 'permission denied' the user was 'loginuser'.

You need to login as su (superuser / root) after a login as loginuser. The default password for superuser is admin.