Andrew:
Thanks for reaching out to the Mom's Panel!
I don't think there's a good or bad way to approach your trip, but with the ages of your children, I'm inclined to recommend that you begin your trip at
Magic Kingdom--because those characters are what's most familiar to your children--and then bookend the trip with your second day at Magic Kingdom at the end, celebrating with its night parade and fireworks.
Another approach, because of the length of your stay, is to visit
Epcot on the days you believe that the parks will be at their most full. Typically if you're going in warmer months, crowds are heavier on weekends. Epcot's sheer expansiveness disperses crowds. However, this is opposite my recommendation for a fall trip. The
Food & Wine Festival at Epcot packs the park on fall weekends from late September to mid-November, and I don't recommend visiting on weekends for families of small children.
If we can help answer any other questions for your trip, feel free to come back and visit!
Whitney