Most people just apply it regularly, I apply every 30 minutes to an hour. The goal is to just keep your lips moisturized, so apply as often as you need to.
You can keep the scabs on if you like, but I took mine off to start a fresh process and I haven't grown flaky scabby skin since.
Also make sure to dab the Aquaphor on your lips rather than rubbing it on so you don't take any buildup off your lips.