Note: looks like you have to be logged in to see the annotated picture on the FAQ page, which shows where the different size screws go.
Looking at the photo, I’d guess that:
two of the 12mm screws go under each pickup offset diagonally;
The two 19mm screws are inserted from the top in the two remaining diagonally offset holes in the neck pickup; and
The two 25mm screws are inserted from the top in the two remaining diagonally offset holes in the bridge pickup.
Take a look at the FAQ photo to confirm.