Arq can be configured to back up to multiple destinations. Each destination has its own configuration, so you can back up some folders to 1 destination and the same or different folders to a second destination.
To add a destination, open "Preferences" (from the "Arq" menu) and click the "Destinations" tab.
Click the + button to add a destination. Enter your Amazon key pair, or click the pop-up button to change from "Amazon Glacier and S3" to a different option and fill in the relevant fields.
When you've finished adding your second destination, you'll see both destinations in the main window. To back up a folder to your new destination, select the new destination and click the "Add a Folder to Backups" button.
Your folder will appear under the new destination: