Looking for a duck boat and I was curious what kind of boats ya'll use, I'm not looking for a cabin cruiser in camo but want a aluminum boat that can handle the chop and slop of the big rivers like the Potomic and Patuxant not to mention the flats of the Chesapeake Bay. I'd like to be able to put the boat in the back of the 3/4 ton long bed Chevy. Kinda looking at the 16 foot deep V Tracker guide, think the flatbottom ones will get tossed, in the big rivers, flats, and back bays of the chesapeake.

16 ft V sounds like the way to go for what want. Just paint it up camo. There are plenty of ideas to make it into a blind if you'd like. Make sure you have enough power a 20 or a bit better would be good but don't go too crazy.
Do yourself a favor , invest in a trailer. My first 7 years or so I went cartop and later pickup bed. A trailer makes it so much easier especially at the end of a long day on the water.