I have same problem on my 14' flat bottom Stumpnocker. There is no way to make a well on it, unless I want a hump sticking out the bottom of the hull.
The boat runs very level on plane and idle speed, which is good for draft, but not good for the water inside the deck. Your problem sounds the same.
I have only one solution, and it is a product that I used for over 40 years to drain my boats, and it works great, IF, it fits your boat, it is the Moeller Auto Flapper Drain Plug Set 51011-10, see
http://www.amazon.com/Moeller-051011-10-DRAIN-SET-AUTO-FLAPPER/dp/B003E1ZGKG
I had a 1973 23' Formula, and later a 1984 30' Scarab over a period of 17 years, and using that same Moeller self bailing plug I never had to use or replace a bilge pump again.
In order to install it on my Stumpnocker, I'll have to change the drain hole parts, as it has a Garboard type drain, and these flappers are designed for a 1" tube drain.
The way it works is that when the bow goes up, the water drains to the back and out the drain, it is like a one way valve. In all my years of use, never once did it get something stuck in it and allow water back in.
In the case of my Stumpnocker, because it is a flat bottom hull and it runs level, in order to get
every last drop out of the deck, I would have to knowingly make the effort to drain it by riding the boat bow high to drain the water, and also rock the boat from side to side to move the water from the sides into the middle drain. NOW, the boat bow can only be ridden high if I go slow, and being a flat bottom boat, it may not drain going slow. The only way to test it is to put a temporary drain plug (a rubber or soft wood stopper) on the inside and manually drain the boat and see if it works. If it does, then I'll change the drain plug design and buy the Moeller.
Another benefit of the Moeller device was that it was left on the boat, and if it rained on the boat while it was on the trailer it would drain. AND you will never have to remember to install the drain plug, so, you can't sink the boat by forgetting to put in or take out a drain.