If you login FTP as the main domain owner, you should be placed in directory where you will see a html and cgi-bin. You will put your webpages in the html and your cgi-scripts in the cgi-bin.
If you back out one directory you will be in the main home directory where all the domains user directories are located.
Back out another directory and you will be in the domains base directory and the hierchy will look as follows:
bin dev home lib root tmp usr var
The home directory is where you just came from. The var directory is where you will find the spool directory for your mail. You do have ownership of these files and can access them if needed. The other directories have system files located in them and you dont have permission in the unix system to change or view these.