Nothing changes unless you use manager to receive the config first, in which case poof you've just taken a backup. Unless you count things like login and DND states, but those are trivial and will have changed by the time you want to do a restore of any backup taken the previous night.
Setup your backup process to backup whatever is in the manager folder (or set the working directory for config files to be a folder that contains other stuff that you want backed up). So what if you wind up backing the exact same config file up several days in a row? You'll always have the latest config on your backup medium.
Peter