Some people would say that you’re doing something wrong by using Duplicati, because they’ve had problems restoring data and it’s very slow, so if you’ve never had to restore data before you should test that to check that it works, and maybe switch to something else like Borg to be safe.
Also, backing up the folder without stopping the containers first might result in any backed up databases being corrupt, so if you’re running anything that uses databases, you should stop those containers before backing up the folder.
I’m not sure, but I think you’d just need to create a script which stops them, runs the backup, and then restarts them.