Yes, you can usually add offline bookings into travel agency software so everything sits in one place. A manual booking entry screen lets you type in the passenger name, the travel dates, the supplier, the cost you paid and the amount you charged your customer, and the system then treats that record much like a booking made through the portal itself.
This matters most for the parts of your business the portal does not handle for you. A hotel you booked directly over the phone, a bus or rail ticket bought locally, a visa fee, a sightseeing tour arranged with a ground operator, all of these can be entered against the same customer file, so your invoice, your receipts and your reports show the whole trip instead of only the flight.
There are limits worth knowing before you rely on it. A manually entered booking is only as accurate as what you type, because the system has no live link to that supplier, so it cannot refresh the status, pull a cancellation policy or process a refund for you. If the supplier changes something later you have to come back and update the record yourself. Which fields you get, and whether you can attach a supplier voucher to the record, also depends on your plan and on how your portal has been set up.
The next thing to do is open the manual booking screen on your own portal and enter one past booking all the way through, then check how it appears on the customer invoice and in your sales report. If a field you need is missing, ask for it to be added before you start moving your older records across.