Yes, your staff can make a booking for a customer who rings your office, and in the early months most bookings on a new portal are made this way rather than by travellers on their own.
Your agent logs in to the same portal with a staff account and then searches, books and pays much as a customer would, but seeing the prices and options your account is allowed to see. Because it is a staff booking rather than a public one, you can usually settle it in ways a website visitor cannot, for example against the balance held on your account or against the credit you have given a sub agent, and you can record a booking for a customer who is paying you by bank transfer or in cash afterwards.
Two parts of this depend on your own setup rather than on the portal. What each agent is allowed to do, such as seeing cost prices or cancelling a confirmed booking, follows the permissions you give that account. Which payment methods appear in the back office depends on your plan and on what your payment provider permits, so taking a card over the phone may not be possible in the same way an online payment is.
Before you go live, sit with one of your agents and put a real booking through from a staff login from search to voucher, so you know exactly what they can see and how they will take money during a phone call.