If they have Refresh, they start with that many (plus maybe a few more as per this system). If at negatives, I either give them none, or give them a Compel involving their life or plan for each FP I give 'em.
For example, a main villain with a Trouble Aspect of 'Hubris On An Epic Scale' and a -2 total Refresh, I might start with 2 FP but 4 pre-game Compels based on that very thing (having killed an informant who had concealed something they needed, for example)...which can likely be exploited by the PCs. I might leave a couple of these undefined so PCs can make Declarations about them (in which case the NPC gets no FP for those Declarations being tagged for effect...they came pre-paid).
That example is basically what was going on with Grevane in Dead Beat, by the way.
This isn't quite the official way to do it, but it usually works out pretty well.