First of all, you may like to upgrade to the latest and greatest release 3.8.0 as this has some important bug fixes and changes within it.
With respect to the backup question; CatTools has 2 backup activities (although they are not supported on all devices, see our online device matrix).
The difference between these two activities is that Device.Backup.Running Config will issue a 'show running' command (or equivalent depending ton the device) to show the configuration to the terminal window. This is then captured to file and saved on disk.
The Device.Backup.TFTP activity will issue the command to transfer the config to the CatTools TFTP server over TFTP (for example: 'copy run TFTP'... )
Both activities will perform a log in to the device in order to issue the commands. It should therefore have no greater interruption than a manual PuTTY session to the device to do the same job.
To reload the config back to a device, take a look at this: How to: Upload Cisco IOS config from TFTP to device