Bed rails installed wrong?

I bought my short box 03 f350 crew cab used. The bed already had the holes drilled in it but no rails. Now that I have a fiver camper I bought used rails (the Reese universal kit.) went to home depot to get all grade 8 bolts and nuts. And I reused the previously drilled holes. The back rail (closest to the tail gate) uses the actual factory bed bolt holes that go though the sill and hold the bed to the frame. So those two are in the front of the back rail. The other two go to nothing but the bed sheet metal. Now the front rail had the holes drilled in the frame and the L brackets matched up to the rear of the front bracket and bolted no problem. Now the back of the bolts of the front rail went though the bed sill. I read the instructions and it seems as if the set both rails 3" to the back of the truck. Will this be ok to pull a 27' Kountry star? Or should I re drill all the holes and put the rails centre over the bed sills? I afraid if I put it forward it may hit my cab.