Neutral atom quantum computing has emerged as a promising platform for scalable quantum computation due to qubit uniformity, long coherence times, native long-range Rydberg interactions, and all-to-all connectivity enabled by atom shuttling. However, as system sizes grow, complex compilation strategies must be implemented to optimise qubit placement, routing, and scheduling while taking into account physical constraints such as restriction zones, transport limitations, and architecture-dependent connectivity. Managing such a complex scenario requires trade-offs in the compilation design to fully exploit the inherent parallelism of the architecture. This thesis analyses compilation frameworks for neutral atom quantum computers across three architectural paradigms: static arrays, dynamically field-programmable qubit arrays (DPQAs), and zoned architectures.