the only holes you need are for the mounting bolts thru to the frame, the ones with the washers, best you mark from underneath with your bed assembly loosely together .... and that countersink needs to be offset from the bolt hole if you have the correct washers .... the bolts thru the skids go between the boards .... measure the length with the sheet metal together, you don't want them a bit short, measure twice, cut once!
Bill