As next-generation Internet of Things (NG-IoT) networks continue to grow, the number of connected devices is rapidly increasing, along with their energy demands, creating challenges for resource management and sustainability. Energy-efficient communication, particularly for power-limited IoT devices, is therefore a key research focus. In this paper, we study Long Range (LoRa) networks supported by multiple unmanned aerial vehicles (UAVs) in an uplink data collection scenario. Our objective is to maximize system energy efficiency by jointly optimizing transmission power, spreading factor, bandwidth, and user association. To address this challenging problem, we first model it as a partially observable stochastic game (POSG) to account for dynamic channel conditions, end device mobility, and partial observability at each UAV. We then propose a two-stage solution: a channel-aware matching algorithm for end device-UAV association and a cooperative multi-agent reinforcement learning (MARL) based multi-agent proximal policy optimization (MAPPO) framework for resource allocation under centralized training with decentralized execution (CTDE). Simulation results show that our proposed approach significantly outperforms conventional off-policy and on-policy MARL algorithms.