They still have the left/right guys under the leader, but the rest of the structure changed somewhat.
QKDNY was returned to the Persians in HSDS; considering ZWJ was the only one that had a good understanding of it, it's quite possible that the skill was lost to the Chinese Ming branch.
The administration probably consisted of the left and right heralds, plus all available talents organised in whatever form made best use of their talents. At the time of Yang Dingtian, there were three clear standout talents other than Yang Xiao and Fan Yao, so there were three guardian lords (plus the later addition of the purple dragon). Below them were five other standout talents who fulfilled another semi-independent role, but who weren't quite on the level of the guardian lords, and they were grouped together as the wanderers. Then there were the quasi-military flags, each of whom had its own divisions and commanders. The Sun Moon sect of SPW had different personnel, so the organisation would have been different from HSDS.