Do this:
Put the cover on the head.
Place each bolt in a random hole (place, do not screw down).
Swap as necessary.
Each bolt will protrude from the cover by the same amount when sitting in the correct hole (something like 15mm, 1.5cm, 1/2 an inch)
Remember, don't start tightening, just plop them in there and see how far they are sticking out.
If any are sitting flush with the cover before you start tightening they are in the wrong hole.
The two small ones directly over the points cover have washers
Use some light sealant on the cover mating surface as well; I mean light, don't make it sloppy.
Be sure to follow the correct tightening pattern and torque in stages to avoid warpage.
EDIT:
I just realized you should be able to do this exact same thing by placing the bolts into the holes on the cover ahead of time by simply placing the cover on a flat surface
The cam/valves will usually cock the cover to one side until it is tightened a bit.