Well, I don't know if this is the easiest way, but it's the way I did it. You'll need to set the bed back in place (if you removed it) and line it up (make sure corners square, etc). Once it's in, set the boards in place, line them up good and square, setting your bed strips along with them for proper spacing. Then, climb underneath and mark each mounting hole from the bottom with a marker. Once you've done that, you have probably the most accurate measurement you're gonna get. Drill the holes...once you've done that, place an offset washer over the hole (lining the holes up) and trace the washer out. You can then route the countersink. Once this is all done, treat the wood, etc. Good luck!
Regards,
Arizona64