You can use almost any third-party software to backup Espionage'd folders, simply make sure that the software that you're using is on Espionage's white list. Sometimes a backup program will use a helper program to perform the backup, and will not backup the folders itself. It can be hard to locate this helper program, so in that case simply wait until it begins performing the backup, and then once it brings up the password prompt, simply use it to add that program to the white list.
Important: You should only perform the backup on a folder while it is locked. Otherwise the folder may not be backed up, or you may end up backing up the data unencrypted! These headaches could be avoided if you used Espionage's backups.
While most programs should work fine, you may be tempted to use an online backup service with Espionage. While some work, some do not, and some do, but don't if you use them incorrectly.
A general rule-of-thumb is to make sure that you do not use a backup services as a method of synchronizing protected folders across machines.
For example, you can use Dropbox to backup encrypted folders, but you should only do this by using Espionage's backups, and setting the destination location to the Dropbox folder. Do not have folders under Espionage's control reside in Dropbox. In other words, if you see the folder in the folder list in Espionage, it should not reside inside of the Dropbox folder.
The folder, when it is not under Espionage's control (backed up at some location) or disabled, will appear to be empty besides the existence of 3 empty folders that spell out the message: "This folder contains encrypted data. It is controlled by Espionage. Do not modify it in this state."