If your custom domain is set up for mobile deep linking, all QR Codes that have an associated link with that custom domain work just like deep links. Remember that the destination URL has to exist in your mobile app for it to work as a mobile deep link.
You can set your custom domain as your default domain for all new links. If you choose not to, you can also edit the associated short link when you create a QR Code. Change the domain to your deep link-enabled custom domain when you want your QR Code to work as a mobile deep link.