For the benefit of future views with similar questions, I wanted to share my conclusion. Which is that I was asking the wrong question. Instead of asking 'where should I put the hose to get the water out', I should have asked 'why isn't the pump getting the water out'? The reason was that there were a couple of holes in the intake hose, so the pump was sucking air instead of the water. The hose was in the right place the whole time.
I also now know that there is only one compartment for bilge water, there is no well in it, and the water you see under the floor hatch in the cabin is the same water you can see from the stern locker. The deepest part is about 18 inches back from the cabin hatch. I hope this helps someone.