Mine was like you said, stringers on either side of the floor boxes.
Simply enlarge the drain hole from the inner bottom to the bilge enough to accommodate the hose(s) and wires and put the thru hull(s) below the rub rail.
Dremel tool or Roto Zip would be an easy tool for enlarging the hole. I did mine in a half moon.

I guess I'll understand once I tear into her but how do you get the hose to the side hull just below the rub rail? I can't understand how that gets plumbed with the stringers and deck in the way. Or do you run the hose out to the transom?

Thanks! I'm psyched to get that hull water tight and have working bilge pumps in the near future.

I'm horrible at explaining stuff.
The current hole that drains the inner bottom to the bilge will need to be enlarged but big enough to act as a drain hole also with the hose and wires running through it. Or you could simply drill a large enough hole above it to accommodate the hose and wire for the pump.
I don't suggest through the transom, either side just below the rub rail would be easier.
See this thread, note the bilge hose location.
http://www.wellcraftv20.com/communit...=battery+bilge

It's not worth the aggravation of attempting routing the hose through the stringers and penetrating the floor.
Here is a shot front to rear of the starboard side, the right stringer is next to the floor box.
http://i175.photobucket.com/albums/w...Picture214.jpg

If it's an I/O, the bellows is the very first place I'd look. Next would be the thru hole fittings.. and if they are plastic.... REPLACE THEM with metal (Stainless).!!!. Nothing will ruin a day on the water faster than your boat sinking.

So if I understand correctly ...

1. cut the access hatch hole midway to the transom from the rear box, the same width as the box and maybe 12-16 inches long;

2. glue a platform such as an old cutting board to the hull with a quality bilge mounted to it;

3. run the electrical and the pump hose directly back to beneath the battery storage area, next to the transom;

4. come up into the battery compartment storage area with wires and hose;

5. wire the bilge and run the hose out to one side under the rub rail.

Is that it. Sounds like a great solution.

I hope I have it but one additional question is how to create a hatch cover for that hole? Do they sell them at West? Do I create my own? Obviously would want a flush mount ... I'm sure there's a thread on it somewhere here!

There are several choices.
A round one of several different sizes that pops out or screws out or a hinged one usually rectangle with a couple of sizes to choose from.
http://i175.photobucket.com/albums/w...i3/2008-19.jpg
http://i175.photobucket.com/albums/w...Picture230.jpg
http://i175.photobucket.com/albums/w...cture228-1.jpg

On all of my boats I just cut an aluminum plate for the pump to bolt to. No need to fasten to the hull.

http://i175.photobucket.com/albums/w...ki3/002-35.jpg

Great, I think that rectangular cover would be perfect. And a hole saw cut between the batteries for the hose and wiring? Is it a challenge to feed the hose and wiring down to the transom area and bring it up? Seems like close quarters.

If it isn't an I/O and you've checked all thru hull fittings, next check for old screw holes and or any damage from intentional beaching, etc. Marinetex is a good product for repairing those types of things.