First, find out what invisible files there are by going to the Terminal, navigating to your home directory if necessary (it shouldn't be), and then typing ls -laF. This will give you a directory listing that includes the invisible files and directories.
Now, open Backup and select File -> Add... When the open sheet comes up, the invisible files will be, well, invisible. Now, simply type tilde (~) which represents your home directory, slash, then the name of the invisible file. For example, to add the previously mentioned .gnupg directory, type ~/.gnupg and press the Choose button. The invisible file or folder is now added to your backup items and can be turned on or off like any others.

