Bonding pad over active (BPOA) layout, which stacks traditional horizontal structure pad electrodes vertically above the active area, is an area-effective device architecture and packaging-enabled solution for GaN-based HEMTs. In this work, the dynamic switching and electric field distribution of such layout, as well as associated capacitance-voltage and trapping characteristics, are comprehensively studied on D-mode GaN-on-sapphire HEMT by performing numerical simulations. In terms of different pad electrodes covering the active area, BPOA is composed of various structures such as gate-related and drain-related BPOAs (i.e. G-BPOA and D-BPOA), among which G-BPOA exhibits inferior switching characteristics due to the additional introduction of Miller capacitance that prolongs the device switching, while breakdown voltage of D-BPOA is 400~900 V lower than other BPOA counterparts due to the interplay between D-BPOA and the drain electrode. Furthermore, the effects of trap capture cross section and trap density on switching characteristics are evaluated. These results highlight the differences in electrical characteristics of various structures within the BPOA layout, and provide valuable insights into BPOA device design and performance improvement.