Please - don't try to do everything in 5 days. I promise that you will be sorry. The worst thing you can do is get tired out and cranky - there will be no Disney magic after that happens.
Get up early every day that you are going to a park. If onsite, take advantage of your morning EMH privileges. After that park starts to fill up, hop somewhere else or take your mid-day break. If offsite, avoid any park with morning EMH that day. At any rate, don't try to go too long into the afternoon, especially with your young kids. Get out and get lunch, get back to your room, take a short nap, and maybe a swim. After about 3 hours (avoiding some of the busiest and hottest time of day in the parks from noon to 5 pm), get back to it. You (and more importantly, your 2yo!) will stay fresh the whole trip, and you'll be touring in the times when the waits are the shortest. If onsite, take advantage of your evening EMH to see even more on short waits.
Following this strategy, you will be able to experience all of the major attractions of all four parks in your 5 days without exhaustion. Plan on coming back, since there is so much to do beyond the highlights!
One note - make sure the kids understand why you are taking mid-day breaks well ahead of time. Prepare them for your trip by talking about your plans with them and why it's important to pace yourselves. Otherwise you may wind up with full-scale rebellion on your hands.
I recommend getting the Unofficial Guide to WDW and planning to follow its touring plans (with appropriate modification). Take advantage of the early morning and late evening periods when waits are short to maximize your chances at the headliner attractions. Do not waste this valuable time doing anything but riding big rides (or ones that build long lines like Dumbo, PPF, or Winnie the Pooh). Take advantage of baby swap where available. Do your homework - know the parks ahead of time and what you plan to do so you do not waste this key time planning instead of doing.
Assuming you are doing 4 days in the parks, I would spend a total of 1-1/2 days at MK, 1 at Epcot (you won't really get to enjoy WS much, but that's the price of a short tour - besides, small kids tend to find it boring), 1 at MGM, and 1/2 at DAK.
Have a great trip, and keep the emphasis on having fun rather than getting things done!
Tim, who wishes he was riding RnRC right now instead of sitting in his office typing this.