This is a brief explanation of the different files and folders that are present in the UNIX account associated with your hosting package.
This is an advanced topic, it requires some knowledge, e.g. about the UNIX Accounts and file system, Apache's log files, etc. You only need to read this chapter if you want to make some advanced customizations of your site or the web applications you installed in your account via the Control Panel.
So most of your files are located in the home directory of your UNIX user: /home/username.
The most important folder in your account is /home/username/public_html. It contains the webroots of the different subdomains you have in your hosting package. For example if you have the www and download subdomains you will have the /home/username/public_html/www and /home/username/public_html/download folders. If you put a file named mypage.html in /home/username/public_html/www/ then it will be accessible over the web via the following URL: http://www.example.com/mypage.html. You should place CGI scripts in the cgi-bin subfolder of the webroot of the respective subdomain.
You will be uploading your site to /home/username/public_html/www and this is the complete UNIX path to your site's webroot. If you're installing a CGI application that's asking you for the complete UNIX path to your cgi-bin folder you should enter /home/username/public_html/www/cgi-bin
The Apache log files can be found in /home/username/logs, they are owned by root and you have only read access to them. There is a pair of logfiles for each subdomain you have (including the www subdomain). For example if you have a package for the example.com domain and have the www and download subdomains you will have the following log files: www.example.com-access_log, www.example.com-error_log for the www subdomain and download.example.com-access_log, download.example.com-error_log for the download subdomain.
The /home/username/etc folder contains a copy of the system's passwd and group files which is used by the chroot-ed FTP server to convert user and group IDs to user/group names. These files are not required for your account to work properly but if they are missing you will only see numeric IDs when you access your account with an FTP client.
The /home/username/htdig folder will contain HtDig's search databases if you've enabled this feature in the Control Panel. Feel free to modify the htdig.conf file in this folder to suit the needs of your site
Remember: this file will be automatically overwritten by the system if you disable/enable the HtDig application in your Control Panel. So if you modify your htdig.conf you should make a backup copy of it each time you modify it.
The /home/username/webalizer folder contains the configuration and data files for the website statistics engine for your package. There is a separate configuration file for each subdomain you have. If you're familiar with Webalizer's configuration feel free to modify the conf files (you should never touch the other files)
Remember: the conf files will be automatically overwritten by the system if you disable/enable the statistics in your Control Panel. So if you make your custom changes you should make backup copies each time you modify them.
The /home/username/yafm folder contains configuration files for the File Manager of your Control Panel. You should never have to modify any files in this folder.