How can travel agents offer lower fares than what's listed at online travel sites?

Travel Agencies generally pay upfront to the airlines for certain amount, let's say $10000. Now, they can issue any ticket as long as their amount is sufficient, using the GDS system like Amadeus or such. Using these systems shows the actual fare and fuel surcharge (Fare + fuel surcharge => total amount) from point A to B. Further, the agents also receive commission which is fixed using the GDS system. In some cases, the airlines also issue paper-fare which is circulated to the stockists(agencies that have pre-deposited amount for tickets purchase). This is the most common way that agencies are able to offer cheaper fares than the online systems. In not so common case, Agencies are able to issue bulk tickets like: when you issue tickets for 10 passengers as a group, they may get 1 ticket free of cost (still have to pay for the fuel surcharge). This depends upon the airline rules. But, these are the internal workings however, ticketing agents have to go through a really difficult IATA examination which includes knowledge about routes, fares, airlines codes and laws etc which helps the agents to work on the best rates to offer to the clients.