If your customer booked multiple trips under one reservation number, but instead of paying for the entire amount, prefers to pay on a per-trip basis, then here's an effective way of doing it.
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1. Go to the reservation number

2. Select the trip you want to charge and click on Edit

3. Go to the Money tab and click Charge Customer

4. The amount for that trip should show on top. Enter the value, select a payment method, add notes (if applicable), and click on Charge Customer.