Joel,
Imagine the box in a box replaces cribbing.
The inner walls of the cribs are the walls of the inner box. The outer walls of the cribs are the outer box. You add rock between the boxes and on the outsides to protect the structure from movement.The outer box has drain holes so any water maintains the same height as the river.
The tops of the boxes may or may not be at the same height. Usually the outer box top is slightly above the mwl (mean water line) and the top of the inner box is 3' above the mwl. You build your boathouse on the inner wall top. You of course opt for a lower inner wall if you feel a need for the boathouse structure to be closer to the water. Clear ?