There's always a Bitly link associated with your QR Codes. If your custom domain is set up for mobile deep linking, all QR Codes that use your custom domain for that link are enabled for mobile deep linking. 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 and QR Codes. 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.