The offset holes are associated with the bed mounting to the frame. Given that you are working with an S10 conversion the "standard" board location may not match up with your frame.
In addition to lining up with the mounting holes in the frame make sure that the holes line up with holes in the cross sills. I recently assembles my bed only to determine that I needed to loosen most of the bolts to shift the boards to allow those frame mounting bolt holes in the boards to align with the holes in the cross sills.
