root has full file access, so if you log in as root, you can accomplish everything you want.
That is how I access all my SME servers for any system modifications.
And if you are using window$, I would recommend using filezilla (
http://sourceforge.net/projects/filezilla/ )
Filezilla has many options that you can't do through window$, ie. file permissions.
I'm not sure you can access all the files via FTP. I would still recommend trying SCP.
If he is inside the lan, FTP is a faster option, faster transfer since no encryption is involved.
From outside of lan, SFTP is a wise choice.