Jon--just finished my second bed last Saturday. The cross sill closet to the cab is free floating. The rubber pad goes under the wood block on the 2nd sill closest to the rear.
Do not tighten anything until all wood is in place and lined up square. 12" bolts in the front 2, and 6 inch in the rear 4 holes. You also need rubber pads on the rear sill. That's how I did it with parts from Mar-K--they are the best--Bill