Hi. We just went this past June.
You have to visit Magic Kingdom at least one day, if not just to ride the tea cups. Your boys would most probably like Tomorrow land (buzz lightyear) the most, and its right next to Mickey's Toontown and Fantasy Land which has the classics.
Your boys will also like Hollywood Studios.
For food, you make food reservations way in advance. Trying to make last minute dinner reservations is a joke. We tried it one night at 6p and were told we couldn't get a reservation to a restaurant in our hotel until 930p.
If you fly in, there is a series of buses that will pick you up and take you to your Disney property. The signs for this, in the airport are not very clear. The pickup location is in the terminal on the first level.
If you drive, stop at Walmart and stock up on water/snacks, etc. A bottle of water is $4 a piece. Staying at a Disney property, you'll be able to charge everything except meal tips to your room. They will require you to have a credit card on file at check in, for this purpose. (found this out at checkin!). If you stay at the Contemporary, Polynesian or Floridian, getting to/from Magic Kingdom is a breeze! Getting to other parks there is a bus system, but it has long waits and driving there is usually faster. You'll have a parking pass so you won't have to pay throughout the system.
If you can afford the Park Hopper do it. If you can get the meal plan, do it. It saves you a ton of money at lunch and especially dinner! Its amazing! Also, each park has special 'before' or 'after' hours just for guests staying on Property.