To answer your questions directly about one or two SQL instances for WSUS. Is that it will cause conflicts between the two WSUS Servers if they share a db. Aka if some deploys an software update (SU) on WSUS, it will get installed on CM clients too (outside of CM control). From the CM standpoint, CM will change that products and classifications existing within WSUS, including declining SU too. Thereby stopping any WSU deployment of that SU.