I've done a number of them, in 14' and 16', some Jon boats, mod-V and full V-bottoms.
In all of them, I went with the platform at the seat height, and they worked great. Some guys make them at gunnel height, and I don't like that at all.
I don't have many pictures, but here are a couple of my 16' Princecraft:
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It had 3 bunks that I put 5/8" floor-sheathing rated plywood. I sealed it well with Thompsons and put carpet over top. [ATTACH=full]124207[/ATTACH]
Later, I added a rear deck between the floatation seats/bunks at the same height and section of flat flooring in the forward area. I never did the flat floor in the back.
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This is a 16' factory Tracker TX, re-decked. They make their decks higher than I like, but no issues with balance. Still, it's a lot easier to step off the edge, if you aren't looking. At least there is a little lip to help warn you.
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Sorry, I don't have many pics in this computer.