I agree that you should do a split stay. Since you will be there for 6 nights, I'd recommend 4 nights at the Poly followed by 2 at AKL. AKL is self-contained and land-locked, so the shorter part of the stay should be there. Plus, you may feel rushed and short-changed at the Poly if you leave there too quickly. And I think you should end the trip at AKL because you will probably be park-focussed when you first arrive at WDW, whereas by the time you get to AKL you may want to kick back a bit and enjoy the resort and its superior restaurants. Those two resorts have my favorite pools. Even though the BC is my favorite resort (followed closely by your two choices), I'm probably one of the only people in the world who don't care for Stormalong Bay.
Enjoy the trip, whatever you decide!