Updaft plus for Backups

In my multisite I made a site (not finished yet) clints.freedomwave.net and I mapped that site to fightingthefish.com so he wanted a different URL http://www.clintscustombaits.com so I set that domain up and I used updraft plus to back up the site at fightingthefish and then upload it to the new domain clintscustombaits.com so it was super easy but unfortunately the updraft back up only backed up my main domain on my multi site http://www.freedomwave.net. So now I am super confused I need to make back ups but they are only backing up the main domain on the multi site. Any ideas? I gained support access and I really appreciate any advice!