Selecting seat on your flight with agent

As a former travel consultant can I just say that if you started the process through an agent, then make all future dealings (eg seat requests) through the agent. It's a recipe for confusion if you start doing some things with the agent and others with the airline direct.
Just call the agent, they can book the seat for you. You can use seatguru to figure out what seat would be preferrable. If not, the agent can see the seatmap and arrange a seating number for you.
The agent should have given you a full itinerary (which should have included your booking reference) as soon as your flights were confirmed.