Hi Erin,
Try to plan your day around your children's regular schedules and try to mirror that with your planned park activities. If your kids are full of energy in the mornings, take advantage of that and get an early start. The parks are less crowded first thing in the morning, mitigating your time spent in line.
You can either treat each park as its own day trip, or you can try to do one park before naptime and a different park after. When my daughter was 2, we would wake up early hit rides and shows, go to a sit down restaurant for lunch, and then back to our room for a nap. We would go back out after the nap, but we'd be sure to return at her normal bedtime. We also brought books to read to her before bed so that she would have the same routine.
We let our daughter's mood be are guide most of the time. If you go on three rides in a row and the kids seem to be getting cranky, consider taking in a show like
Playhouse Disney-Live on Stage or
Mickey's PhilharMagic. We also find that the table service meals are great for everyone to unwind, relax, and color.
Hope that helps
Michelle