Thanks for all of the suggestions and advice guys. So what I gathered from your advice, 6' x16' boxes would not be a good idea. I went by the rock supplier today and what he has is much to large to use for this- not to mention that it's $90 yd. I calculated the cost if I purchased the bags from HD as mentioned and if I built one 16' x 16' box it would require 214 bags at a cost of about $830.
Looking at the pictures that you have posted, would just sand work? The first picture looks like a sandy pond bottom. Thoughts?
Dean