It gets applied to your onboard account, so any charges that go to that account. Anything like gratuities, excursions, tastings, beverage charges, souvenirs, etc. to to your onboard account. You don't really "apply" the OBC, it just comes off your total balance. Placeholders are a separate charge directly to your credit card.
Be aware that you only have 30 days to transfer a reservation to a TA, and many TA will give a reduced OBC for transferred reservations vs those made directly through the TA.