Hay wagon rub rails

So I got this running gear which I understand and 2 stringers which I understand and these 2 16' long metal u channels dimensioned 3 3/4" deep by 3 1/8" across the back or bottom. I think it is rub rail but it has stake pocket holes. I know I need to bolt top, bottom, and side to bed, but how to drill, cut the stakes holes and still maintain structural integrity? I am laying the deck lengthwise but do I nood to change to crosswise? http://photos.yesterdaystractors.com/gallery/uptest/a128478_sml.jpg
http://photos.yesterdaystractors.com/gallery/uptest/a128479_sml.jpg
http://photos.yesterdaystractors.com/gallery/uptest/a128480_sml.jpg
Little Help Here? I gotta get started the weekend so help ASAP. what about adding wood inside the rail and the bolting it on. What to do?

Do you see the pieces of wood that is still inside the rails? That is how thick your cross pieces are supposed to be minuse the piece of flooring that is still inside the box on top of the cross pieces. I can see that in your pictures. Just put the floor out only to the inside edge of the stake pocket holes. The little piece of angle iron at the stake pocket holes goes on the bottom and that is to keep the thin edge of that steel from wearing into the wood stakes for the wood sideboards (Some beds had steel stakes and steel sideboards instead of wood). Taper your cross pieces to fit inside of that steel rail from the point that the cross pieces set on top of the sill. And you want the floor to run lengthwise and not cross wise. That is exactly the same as the steel flat truck beds except for the fact that some had steel cross members in instead of wood. And it is a rub rail to keep you from busting up the ends of your cross pieces. Should be by looking easly seen how they go. And that was a very common way for the factory built beds to be made if they were a good quality. You should see what the bolts look like from the bit of cross pieces that are still in them and cut off. Exactly what I had told you earlier. Can't put pictures on or would show you a picture of one of the beds but I could snail mail you a picture.

Ok, I see it now. I was confused also about how they would go, but Leroys explanation makes perfect sense. I have seen that on old truck beds now that you mention it.

Thanks guys I think I got it. Gonna look for pic of old truck beds to be sure. Started working on another on paper will post when I get work drawings.