You can add a payment to a trip whose bookings are already marked paid. Switch on the option to apply the payment towards paid bookings and every booking on the trip becomes available for allocation.
When the amount you collect is higher than the amount due, you choose where the extra goes. Spread it evenly across the tickets being paid for, pick the specific ticket numbers it belongs to, or put it on a new invoice item that you name.
The additional payment appears at the bottom of the invoice as a payment with a receipt. The same flow is in the manual transaction form on the trip, the invoice and the financial views.