I am looking to a solution to covering my boat when, I am not using it. I have a 16ft flat bottom jon.  In the past I have used tarps and tried to have some kind of beams in the boat so the water would run out. I have had a problem  with the weight of the water being too much and its a real pain  to get the tarp out. The only part that is flush or higher than the rails is the steering console.  I  usually just suck up the time and clean it out good, but I plan to mod it this winter and try and make it more like a bass boat and I don't want to put all the time and money in it, just to have it ruined. Any suggestions would be greatly appreciated and taken to heart.

You need to get it raised and sloped somehow. make some braces/ stands to get a taper on the tarp. Sloped toward the back or sloped to the sides should work.

Bps catalog also has some device for this. I don't see it online but might give you an idea to look at one close bye.

I'm assuming it's on a trailor. Is there anyway of turning it upside down on the trailor.

You could make something like this.

http://www.boat-cover.net/Attwood_Deluxe_Boat_Cover_Support_System/dm/session_id.880352821--cart_id.508049361--category_id.216555--list_time.1195286074--view_id.38580

PVC tent = cheap and effective!