Once the screw holes were all drilled, I set the nut plate in place. Due to the angle of the fuel neck I had to position one of them on the top of the flange to drill the holes for the nut plate. The rest I positioned on the correct side. As I drilled each hole I used the screw and a clecoe to hold it in position. Clecoes worked for drilling the holes, but not for setting the rivets. The clecoe tends to pull the plate nut down on one side and raising the other instead of holding it flush to the surface. So after I put in all the counter sinks, I used the rivets to position the plate nuts and a cleco clamp to hold it down flush. This worked really well.
plate nuts in place, ready to drill
screws keeping plate nuts in position
used cleco clamp rather than clecoe prior to setting rivets