This paper presents a two-layer control architecture for coordinating a swarm of drones equipped with heterogeneous sensing capabilities to efficiently and continuously monitor targeted areas distributed across a large area. In the first layer, the targeted areas are clustered into several regions approximated as convex polygons, where the drones will be allocated to these regions. For this allocation, a novel optimization problem is formulated to balance the trade-off between minimizing uncovered areas and ensuring equitable coverage across regions. The second layer enables drones to persistently and safely monitor the targeted areas within their assigned regions. Simulation and experimental results validate the effectiveness of the proposed architecture using a small-scale drone swarm to demonstrate the monitoring performance, including enhanced coverage and reduced travel distances for the drones.