New bed wood, what am I missing here...

[Chevystep]

I know I ain't the sharpest knife in the drawer, but I read about these beds being re wooded off the truck. How the heck do the crossmember supports that bolt to the frame end up being in the right place to line up the long bolt mounting holes? None of the prepunched square holes on the side flanges are close enough to just line them up with those. I've got my longbed step sides and rear all put together and squared up, but it seems I've GOT to line up at least the rearmost V notch mounting spot on the rear lower tailgate piece with the frame hole, then mount the wood and make sure the crossmember pieces line up with the frame hole as the wood goes in....am I missing some trick or should the bed strips and side flange holes make everything match up when assembled off the truck..??