In general, you won't even notice whether files you are using come from AFS or not. The time when it really does make a difference, however, is when you want to change file protections, and this is critical since your Athena home directory is in AFS space.
If you wish to list or change protections, you will need to become somewhat familiar with the program fs. This program allows you to get various kinds of information about AFS files and directories and to change and look up protections on directories. Although it is not necessary for you to understand standard UNIX file protections in order to understand AFS file protections, it will probably help you if you do. Standard UNIX file protections are explained in the File Protection section of this document.
The fs command has a built-in help feature. Typing fs help will give you a lot of information on how to use various subcommands. All the commands that you will probably want to use, though, are described here.
Luke Faraone 2012-01-11