As fast as these SSD drives are, you're fine putting everything on the SSD drive and let that clone to the backup SSD drive - but in a well organized folder structure for each project that might go on the primary, external SSD drive.
That said, Carbon Copy Cloner can clone drive to drive, drive to folder, folder to drive, or folder to folder. With a 1TB primary SSD and 4TB backup SSD, you could use Carbon Copy Cloner to clone the source media folder from the 1TB primary SSD to the source media folder backup on the backup SSD and the project files folder from the Macintosh HD to the project files folder backup on the backup SSD. So, folders to folders instead of drives to drive. You could even set a quota limit for Time Machine in the System Settings and let that use some of the 4TB drive as well.
For Carbon Copy Cloner (CCC), I'm suggesting just a clone rather than incremental back up (so if primary folder and backup folder always match), but CCC other options for how the clone process behaves that you might want to look into.
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