I don't know if you know how to use symlinks. Easiest way is to create one shared folder and name it something like backup. Then create symlinks for all the shares you want to backup for that backup folder. You can then use a Rsync job to backup the shared folder with -L option. The -L option follows symlinks and backups everything in the linked shares. I believe the usb backup uses Rsync and you can use the -L option in the extra options field. You just have to make the correct symlinks in the backup shared folder.
ln -s /media/UUID1/share1 share1
ln -s /media/UUID1/share1 share2
ln -s /media/UUID2/share3 share3
Then setup your usb backup job with the -L option in the extra option field.
You will use the backup shared folder to the external drive.