Jenny,
Sounds like somebody has been good over the holidays!
So for a place to stay, I always recommend Port Orleans Riverside for the moderates. Now if you have some Pirate enthusiasts you might consider the Pirate-themed rooms at Caribbean Beach, but I still think that unless they are so gaga over that movie that nothing else will do, I would still stick to Riverside. More to do, and boat access to Downtown Disney and the resort bus service is nice.
As to the two parks, the first is always the Magic Kingdom. ALWAYS!
The second obviously depends on what your boys like, and how old they are. But I would say your choices are either Hollywood Studios, or a second day at the Magic Kingdom. I would opt for the second park, but if you have younger boys they might still have more that they want to do at "the Kingdom".
Send me a follow-up question and let me know what you think. We can work on some ideas of where to eat, whether it is table service, quick service, or even some yummy snacks on the go so that you get as much attraction time as possible.
Have a magical vacation!