Hi! Ok, so here is how we decide where and when.
First we find out the park hours for the days that we will be in WDW. Then we check the Extra Magic Hours for those days-I make a little chart with all the hours for each park/each day. I use the unofficial guide site for the Best Parks and parks to avoid for each day. Once I have that filled in, we start thinking about what restaurants we want to eat at.
We eat breakfast in our room, unless there is a special place we want to try for breakfast. We usually have one table service and one counter service per day, but that is just us, everyone is different. You can see all of the restaurants on allears.net, look under dining. If we are eating a table service at lunch time, we tend to go for 1-2pm, especially if we might have been at late emh the night before. For dinners we might schedule anywhere from 6-8. Sometimes it will depend upon when the fireworks will be, and the parades, and if that is important for your family, like if we eat at the California Grill, we want to be there for the fireworks at MK.
That is why I make a chart with the times, and preferred parks, special shows like off kilter at Epcot or Flower Power Concerts during the spring. Then we can really "walk" through our day in our head to be sure that we aren't making things too tough on ourselves and are allowing enough time for transportation to and from parks.
We will be happy to help you, looks like you are going in October? Great time of year!

Hope this helps!