We just got back from 10 days at the Fort and didn't spend nearly as much time there as we thought we would. Our boys are 3 and 6 and want to spend as much time at the parks as possible, and this was our third trip in a year. We always get up early so that we're at the park when it's open, then come back for a nap and swim between 1:00 and 2:00, then back out to the parks after eating dinner at the RV. They're able to stay up late until park closing/fireworks after having their nap. We don't take down days at the Fort, only down afternoons or mornings.
We find that Early Magic Hours at the parks are better than late ones, because the kids usually can't stay out that late anyway, plus it's a lot less busy in the mornings. We're usually leaving the parks when they're starting to get busy just after lunch. We like going to Epcot in the evenings. It's usually not too busy, and the only problem is that the Fastpasses for Soarin' are usually gone by the time we get there and we won't stand in line for an hour.
We found that Hollywood Studios was our least favorite because they don't have as much for younger kids. You can pretty much do it in 3/4 of a day. We never go back there in the evening because it's so busy that we can't get on most of the things we want (Toy Story Mania) and it closes earlier than Epcot and MK. Animal Kingdom is the other park that we go to first thing in the morning because it closes first. You can do most of it in 3/4 of a day as well.
You'll probably want to spend more time (1 1/2-2 days) at Magic Kingdom. There are so many rides there for younger kids and it's our favorite. Again, go first thing in the morning as soon as it opens and head straight to the rides you really want to go on (ie. Dumbo, Peter Pan) because they just get busier and busier as the day goes on.
I highly recommend the book The Unofficial Guide to Disney and read it before you go. It has a lot of great info in it about which rides are the busiest, which order you should do them in, etc. We don't follow their touring plans because we only go to Disney when it's not that busy but I can see that it would be really helpful if you went during the busy season. I would plan which rides you want to go on and in which order before you get to the park. It will save you a lot of time.
Also, don't forget to use Fastpasses and rider switch if there's something your older child wants to go on that your younger one isn't tall enough for. My oldest son loves being able to go on rides twice in a row without having to wait. It's awesome. And another tip we found out on our last trip. If the Fastpass tells you the return time is between 11:00 and 12:00, you can return anytime after 11:00 until the park closes. We never had a castmember turn us away when we did this and it was so nice to return when it fit into our schedule.
