Can I add my customer's frequent flyer number and passport details to a flight booking on my portal?

Yes, in most cases you can. The passenger screen on a flight booking normally has room for more than the name, so you can enter a date of birth, a passport number with the country that issued it and its expiry date, and a frequent flyer or loyalty number for the airline being flown. Those details go to the airline with the booking and sit on the airline record itself, not just in your own notes.

What the airline does with them is not the same everywhere. Some airlines want passport details before they will issue the ticket, some are happy to collect them at check in, and many only ask for them on international journeys. Frequent flyer numbers are usually accepted at the time of booking, but whether the miles actually land in the account is between your customer and the airline, so it is fairer to tell them to check their account after they fly than to promise anything.

Budget airlines and some fare sources are stricter or simply accept fewer fields, and a number that is mistyped may be quietly ignored rather than rejected with an error you can see. If you find a field you need is missing for a particular airline, that is usually a limit of what that supplier accepts rather than something on your side.

The sensible next step is to make one test booking with a passport and a loyalty number filled in, then look at the airline reference to confirm the details came through, and ask whoever supplies your fares which fields each of your suppliers passes on.