Once you have made a booking for a customer on a session or course it's simple to mark the booking as having been paid offline, as free or to debit a credit from a package.
Access the booking record by clicking on the customer base in the Attendees tab of the session or course. You will then be presented with options to take payments, the default of which should be any package that is live on their account. If the package displayed is not the one you want to debit, simply use the arrows to scroll through the different payment options. With the desired payment option/package selected just click Debit this package and a credit will be debited from the selected package and the booking marked as paid. The debited package will now show as the Price paid in the Attendees tab.