Our fmsa server is on a virtual machine. Our users have mapped drives to file servers that have fairly robust backups. Can we store our on the mapped drives that are not of the fm server machine?

Yes, you can do this, but you need to remember that the user SuperContainer is running as (which might be FMSAdmin, SYSTEM, or FMServer) must have permission to write to those shares. You will configure your SuperConatiner's web.xml file or the options if you are running in stand-alone mode to specify your share location.

The permissions to make your SC able to write to this can be rather tricky, so it may take some configuration on your network to get it to work.

Keep in mind that you do not want to give your users access to the files which are stored on your SuperContainer server. If you store your SuperContianer documents on a particular share you will want to make sure that your users do not have access to that share. Documents stored in SuperContainer should be accessed only through FileMaker to prevent desynchronization with your FileMaker database, security issues, and user confusion. Users should not access the SuperContianer documents through their OS, a share, ftp, or any other file transfer system outside of the web viewer and companion plugin in FileMaker.