Use SDxServerManager.exe with the /upgradealldbs argument to update all server site databases in parallel. You can provide information using additional arguments:
/out:[JSON file path] - specifies the JSON file path to output the settings to in JSON format (optional).
This example upgrades all server sites in parallel for an SQL server:
SDxServermanager.exe /upgradealldbs /out:"c:\temp\myjson.json"