To assign credits to a previously checked out booking, if you click into the Daycare booking, and from the left hand menu click on the Admin link;

Once the screen opens as long as there are no credits already applied to the bookings, you will see the following panel; You can choose how many credits to assign to the booking using the dropdown list - you can also set a price for the booking if required if there are not enough credits to cover all pets on the booking.