I am unable to choose where the Spymaster can be specifically targeted in order to counteract against factions.
If you want to target a specific province, you'll have to use the job "Build spy network", which now not only increases plot power & spreads rumours (like before) but also takes the role of dissuading vassals from joining factions.
I'd suggest you take a second look at all old councilor jobs, as we've moved a few effects around, so you're not surprised with some outcomes (or lack thereof !). Although to be faire, the whole Scheme/Build Spy Network is the biggest change.
Arthur