When you say logon window, do you mean the Terminal program or do you mean the thing you get when you first boot up the machine?
if its the Terminal then you would...
1. Enable the root user with Netinfo manager
2. In the Terminal type su - <enter> then the password
3. poof you are root
if you mean the loginpanel...
1. Enable the root user with the netinfo manager
2. make sure that in the USERS control panel you have it set to allow someone to enter their username instead of using pictures.
3. when it asks for username, enter "root" then the password...
For ftp its a bit trickier...at least on my freebsd box it is. There is some stuff you have to edit in the /etc/login.conf file that will allow root to ftp in. This is generally frowned upon because if you logged in as root with an ftp client, the root password would pass unencrypted over whatever network you are on and others in between. Generally a no no.... instead use a normal user to ftp then ssh into your machine, become root, then move your files wherever you like...