Yes, in most setups you can record a booking you arranged yourself and keep it next to the ones made through the system, so a customer's whole trip sits in one file. This is usually called a manual or offline booking, and you type in the details you already have, such as the supplier name, the dates, the service, what you paid and what you are charging. Once it is saved it behaves like any other booking in the file, so it appears in the customer's history and can be included in the itinerary you send them.
The honest limit is that a manual booking only knows what you tell it. There is no live connection to that bus company or that hotel, so the system cannot confirm the reservation, cannot warn you if the supplier changes something, and cannot show a cancellation deadline unless you enter it yourself. If the supplier moves a time or the hotel changes a room type, you have to update the record by hand. Anything you type wrongly will stay wrong until someone corrects it.
Whether these manual bookings also flow into your reports, your customer statements and your outstanding balance list depends on how your account is configured and on the plan you are on. In many cases they do, which is what makes the feature worth using, but it is worth confirming rather than assuming, because some setups treat offline items as notes only.
The next thing to check is whether a manual booking on your account carries through to your month end reporting and your money owed figures, and if it does, agree with your staff on a simple rule for what gets recorded so your records stay reliable.