Can I add bags and seats to a flight booking after my customer has already paid?

Yes, in many cases you can, but it is not guaranteed for every booking and it depends far more on the airline than on the software.

Low cost airlines are usually the easiest. Because the booking stays in the airline's own system, the supplier connection often lets you reopen a paid booking, see which extras are still on sale, and buy them straight away. Full service airlines booked through a global distribution system work differently. Some let you request a seat at no charge, some sell extra bags only through their own website or call centre, and some allow changes only before the ticket is issued. So your portal will show the options the supplier makes available to it, and nothing beyond that.

Where it is supported, you open the booking in your admin area, pick the passenger and the flight leg, and the extras come back live with whatever the airline is asking at that moment. That can be more than it would have been at the time of booking, because airlines often raise bag charges closer to departure, so it helps to warn your customer early. You collect the money in the usual way and the booking is updated.

When an extra cannot be added through the portal, you are not stuck. You arrange it directly with the airline using the booking reference, then note it on the booking so your records match what the passenger actually holds. The next thing to do is ask which of the suppliers on your account support changes after ticketing, and test one real low cost booking so you know what your team can handle in house.