To maintain position you use your fins same as in a tube. This is where the larger profile of a pontoon can hurt when it's real windy.
I fish a lot in the delta with the tides, current and wind. You get used to it.
Set up time can vary depending on which kind of boat you get. Less then 1/2 an hour, some boats as little as 10-15 minutes including inflating pontoons.

I would recommend getting the best boat you can to start with.
Outdoor Engineering's Versa-Vessel is the sweetest boat around(IMO). Quick set up and easily customized. http://www.outdoorengineering.com/

Good luck,
Mitch