Can I record a booking I took over the phone or on WhatsApp in the system so everything is in one place?

Yes, in most cases you can. Travel agency software usually lets you add a booking by hand, so a sale you closed over the phone, on a chat app or with a walk in customer sits in the same place as the ones your website made on its own. That way your sales figures, your customer list and your pending payments are complete rather than split between the system and a notebook.

The way it normally works is that you open the bookings area, choose the option to add a booking manually, and fill in the traveller names, the travel dates, the hotel or airline, the supplier you booked with, what it cost you and what you charged the customer. Once it is saved, it behaves much like any other booking in the system, so it shows up in your reports, it attaches to that customer's history, and you can usually print a voucher or an invoice from it.

The honest limit is that a manual booking is a record, not a live connection. Because the system did not make the booking with a supplier, it cannot confirm, change or cancel it for you. You still do that directly with whoever you booked through, and then you update the status in the system yourself. If the airline or hotel changes a timing, nothing will update on its own. Whether the manual entry screen is available to you, and how much detail it asks for, can depend on your plan and on how your portal was set up.

The simplest way to judge it is to take one booking you handled offline last month, enter it as a manual booking, and check that it appears correctly in your sales report and under that customer, then agree with your team that every offline sale gets entered the same day.