Can't update cfg file on debian 6 Cccam server

Hi,
I've just set up my first debian server and straight away run into a problem that I'm sure there's a simple answer to - I'm probably just blindly missing the point somewhere!
I used Ten Below's excellent autoinstall guide on this forum, FTP'd my config file and now have server, DM800 & Spiderbox all happily recognising each other as client/server.
Now I wish to add more lines to my config but when I connect via FTP, although showing as connected, I cannot view the server files and the new config file just sits on it's own.
I am logging in as "username", as I did with the original first cfg, rather than root as when I try to log in as root with the correct password the connection is always rejected as incorrect username/password or too many concurrent logins.
Anyone point me in the right direction? Cheers.