I have a collection of screws and bolts that I cut off so that they're just long enough to hold a nutplate tightly while I drill the rivet holes. Screw 'er in, drill one hole, cleco that one and then drill the other, then uncleco and unscrew.
#6, #8, 3/16, etc.
I also have a few nutplates that I ran a tap through a few times so that I can use any screw to easily screw it all the way down tightly.
Either way...I have nutplate jigs, but don't like them because I find it harder to get the rivet holes properly aligned. E.g., draw a line from an edge and "over" the screw hole, using any method or tool. You'll never get it *exactly* centered on the hole. With a jig, I always ended up with the rivet holes just a tad "cockeyed" because I can only see one hole/line combo at a time. With an actual nutplate, I can see both, and as long as it looks the same on both sides, I know the nutplate is straight relative to my line.
Crooked nutplates bother my sense of order in the universe.