Many network-wide traffic management strategies based on the Macroscopic or Network Fundamental Diagram (NFD) have been developed in recent years. In this paper we investigate one of these strategies, namely feedback NFD-based perimeter control, which limits the rate at which vehicles are allowed to enter an urban region. The inflow limitation is imposed at selected main entry links (gated links) and results in queuing of vehicles at the boundaries of the network. Most of the works on this subject neglected the effect of the queued vehicles on the traffic conditions upstream of the gated links. In this paper we analyze in microsimulation the queuing at the gated links and its effect on network performance for a realistic network model. Moreover, a queue management strategy based on a continuous quadratic knapsack problem aiming at balancing relative queues at the gated links is proposed. Simulation results suggest that queues under perimeter control are shorter in space and time than with no perimeter control. Additionally, managing the queues at the gated links not only improves the overall network performance but also reduces the possibility of queue propagation to the upstream junctions. This improves traffic flow outside the protected network.