Hi Carrie!
You are going during a relatively slow time of the year, so I wouldn't worry so much about which park you should see on which day. It won't make that much of a difference in all honesty! You might want to take advantage of any morning Extra Magic Hour (EMH), but it's not critical. You can also take advantage of evening EMH, but your children might be too tired at that point. EMH are not that important when the parks are relatively empty and they will be during your visit.
However, a good itinerary would be: Animal Kingdom on the 10th, Epcot on the 11th and 12th, Magic Kingdom on the 13th, Hollywood Studios on the 14th, Magic Kingdom on the 15th, and your favorite on the 16th. I think Epcot and the Magic Kingdom both require 2 days!
I will point out that there will be two offerings of Mickey's Not So Scary Halloween Party in the Magic Kingdom while you are there. It's a fabulous party and my favorite hard ticketed event (meaning you need a special ticket for it) in the Magic Kingdom. However, I don't know if I would recommend it for you. The party runs from 7pm to midnight, which is a little late for very young children. However, your 3 year old would probably love it, if he or she took an afternoon nap.
With regards to attractions, you can actually go on most of the attractions at Walt Disney World with your 3 month old! I know that sounds weird, especially if your only experience is a regional amusement park. However, Walt Disney World was designed with the whole family in mind. There really are only a handful of attractions that have a height requirement. You can get information on which attractions have a height requirement
here. It will be on the right side of the page!
Enjoy planning and write back if you have any more questions!