There are several ways to back up FDM. First, you should also be backing up your FDM application server as well as the relational server. You can also export the application metadata (locations, maps, scritps, etc) to an XML file using File > Export from the workbench.

An FDM application consists of two parts:

a) The Relational Database for the application
b) The FDM application path

The FDM application path should be backed up as well as the relational database associated with the FDM application. I would recommend at least a daily backup of the relational database and application path if possible.