Natural disasters often damage ground infrastructure, making unmanned aerial vehicles (UAVs) essential for emergency supply delivery. Yet safe operation in complex post-disaster environments requires reliable command-and-control (C2) links; link instability can cause loss of control, delay rescue, and trigger severe secondary harm. To provide continuous three-dimensional (3D) C2 coverage during dynamic missions, we propose a Heterogeneous Dual-Network Framework (HDNF) for safe and reliable emergency delivery. HDNF tightly couples an Emergency Communication Support Network (ECSN), formed by hovering UAV base stations, with a Delivery Path Network (DPN), formed by fast-moving delivery UAVs. The ECSN dynamically safeguards mission-critical flight corridors, while the DPN aligns trajectories with reliable coverage regions. We formulate a joint optimization problem over task assignment, 3D UAV-BS deployment, and DPN path planning to maximize end-to-end C2 reliability while minimizing UAV flight energy consumption and base-station deployment cost. To solve this computationally intractable NP-hard problem, we develop a layered strategy with three components: (i) a multi-layer C2 service model that overcomes 2D-metric limitations and aligns UAV-BS deployment with mission-critical 3D phases; (ii) a 3D coverage-aware multi-agent reinforcement learning algorithm that addresses the high-dimensional search space and improves both training efficiency and topology resilience; and (iii) a 3D communication-aware A* planner that jointly optimizes C2 quality and flight energy, mitigating trajectory--coverage mismatch and improving routing safety. Extensive simulations show that HDNF markedly improves C2 reliability, eliminates outages in critical phases, and sustains high task success rates while reducing hardware deployment cost.