Steve:
What year/model is your truck? We have a general instruction
http://www.mar-k.com/drilling_mounting_holes.html that may be helpful. We have written complete bed assembly instructions for many of the trucks which includes more specific information. These instructions now are free with your parts order.
I am always concerned about providing a "layout" type dimension to the bed-to-frame holes. If your wood is slightly different than the wood used for the layout or if your frame is tweaked slightly, the hole is in the wrong place and you have ruined a board. As difficult as it is, using your frame as a reference for hole location is a sure-fire way to get them in the right place.
Mar-Ktech