Yes, in most cases you can. Travel agency software usually groups everything a customer has booked for the same trip under one reference, and from there you can produce a single itinerary document that lists the flights, the hotel nights, the transfers and the tours in date order, with your agency name and logo on it. You can normally email it straight from the booking screen or download it as a file and send it yourself, and you can reissue it later if something in the trip changes.
There are a few honest limits. The itinerary document is your own summary, so it does not replace the documents the suppliers issue. The airline e-ticket number, the hotel voucher and some tour vouchers come from the supplier, and in many cases the customer still needs those to check in, so a good practice is to send the combined itinerary as the overview and attach or follow with the supplier documents. How much detail each line shows also depends on what the supplier sends back, so one hotel may give a full address and check in time while another gives less.
If part of the trip was arranged offline, such as a rail ticket or a hotel you contracted yourself, it will only appear on the document if you record it in the software first. Once it is recorded alongside the online bookings, it sits in the same trip and prints with the rest.
The next step is to make a test trip with two or three elements, generate the itinerary and read it as your customer would, then tell us which fields or wording you want changed on your template.