The GUI version was designed to be a wrapper around the CLI version so it can support only one repository. If you use the CLI version, you can set up multiple scheduled backup jobs, one for each repository, using system-specific task schedulers (for instance, Task Scheduler on Windows and launchd/cron on macOS).
Another workaround, if all your repositories needs the same schedule, is to link all repositories into a master repository using symbolic links. Duplicacy treats the first-level symbolic links that point to absolute paths differently – it will follow them as if they were subdirectories. For all other symbolic links it will backup them as symbolic links.