I use PersonalBackup to do this job.
http://personal-backup.rathlev-home.de/
You can configure it to start cryptomator before syncing and wait a view seconds. Then it starts syncing into the open vault.
You can also configure to start an app after sync is done.
I use it to start my OneDrive client, which then syncs the encrypted files to online storage.
And in addition, you can set up an scheduled task for the complete backup job.
So in my case every two days the following happens automatically
- Start cryptomator and open the vault
- sync local files into vault and encrypt them
- sync the encrypted files to online storage.