So I guess a follow up question I have is do NPCs have a refresh rate in the same sense that PCs do? Is the refresh rate that is mentioned at the bottom of every NPC write up just a gauge of their power, or is that subtracted from the base refresh that the campaign is set at?
I don't know that it is clearly established to my satisfaction, since DFRPG isn't dealing with anything like a concrete Challenge Rating, which is what I was used to. But you can figure something out.
Basically, when you consult the section which tells you how much Refresh to give to an NPC antagonist (based on the PCs' Powers and/or Stunts), take that number as the NPC's base refresh. So if your big bad guy can have 30 Refresh in Powers, then you can spend most or all of that 30 Refresh on powers, and if there is anything left over, then they can have the difference in Fate Points.
However, if you have an NPC/villain in the negative Refresh, you can build up a stockpile of Fate Points by Compelling its Aspects (particularly the Trouble Aspect which is motivating it to pursue its agenda). Each caper that the NPC commits can be thought of as a Compel against its High Concept or Trouble or another Aspect. Making it do villainlike things can expose it to risk or harassment by PCs, but it should get Fate Points for it.
Or, you can just say that your PCs are (say) 10 Refresh, and anything (ANYTHING, including the more powerful White Council Wizards) with 10 or more Refresh spent on Powers/Stunts is a slave to its High Concept/Ethos/etc., and in order to have any Fate Points and earn plot agency, must self-Compel its Aspects, whether it is a "good" or "evil" NPC.