Can I hold a flight for a customer who needs time to pay?

Sometimes yes, but it depends on the airline and the exact fare, so it is not something that works on every booking. When an airline allows a seat to be held, your portal can create the booking without taking payment and show you the deadline the airline has set for payment. Until that deadline passes, the seat is reserved in the passenger's name and you can collect the money from your customer and then issue the ticket from the same booking screen.

The important thing to understand is that this permission comes from the airline, not from the software. Full service carriers booked through a global distribution system are the ones most likely to allow a hold, and even then some of their cheapest fare types have to be ticketed straight away. Low cost carriers almost never allow it, because their system treats the booking and the payment as one single step. So on a results page you may find that one option can be held and the one next to it cannot, and that is normal rather than a fault.

You also need to watch the deadline carefully. If payment is not made in time, the airline will usually cancel the held booking on its own, and when you go back to rebook, the fare and the taxes may no longer be the same as they were. For that reason it is worth treating a hold as a short courtesy to a serious customer rather than a way to park bookings you are unsure about.

The next thing to do is check with each of your flight connections which of their fares allow a booking to be held, and make sure someone in your team is responsible for chasing payment well before the airline deadline arrives.