The evolution of Internet of Things (IoT) into multi-layered environments has positioned Low-Power Wide Area Networks (LPWANs), particularly Long Range (LoRa), as the backbone for connectivity across both surface and subterranean landscapes. However, existing LoRa-based network designs often treat ground-based wireless sensor networks (WSNs) and wireless underground sensor networks (WUSNs) as separate systems, resulting in inefficient and non-integrated connectivity across diverse environments. To address this, we propose Hetero-Net, a unified heterogeneous LoRa framework that integrates diverse LoRa end devices with multiple unmanned aerial vehicle (UAV)-mounted LoRa gateways. Our objective is to maximize system energy efficiency through the joint optimization of the spreading factor, transmission power, and three-dimensional (3D) placement of the UAVs. To manage the dynamic and partially observable nature of this system, we model the problem as a partially observable stochastic game (POSG) and address it using a multi-agent proximal policy optimization (MAPPO) framework. An ablation study shows that our proposed MAPPO Hetero-Net significantly outperforms traditional, isolated network designs, achieving energy efficiency improvements of 55.81\% and 198.49\% over isolated WSN-only and WUSN-only deployments, respectively.