We start with any special events we're booking. For example, our next trip will have a Halloween Party on a Tuesday night. We know that we'll be tired the next morning, so the next day we'll personally schedule a water park, since they are very laid back and they open later. Now, if we were not planning on hitting the water parks, then we would go with whichever park we felt most laid back about, or perhaps Disney Springs or a resort day/morning.
We will probably schedule the day before the party to be at a park that closes the earliest for the same basic reason---to get us some extra sleep before a busy day at MK.
We schedule our first and last days based on what our family wants to see first and do last---total personal preference, no care in the world about crowds. For us, we'll hit MK when we first arrive to do the things that don't require FPs or long waits....low crowd attractions, Sorcerers of the Magic Kingdom, that Pirate thing with the maps that I forget the name of, Tom Sawyer's Island, poking around Main Street, etc. Then we'll head over to Epcot in the evening, because DH needs his Epcot on the first day no matter what.
And the rest we'll fill in based on what's left. We like to split AK in half. That way you get to check out the early morning hours and the evening hours, since the animals tend to be more visible then, and we actually do like the animal portion of AK, LOL! And any free evening we like to go back to Epcot.
So basically that just leaves HS as a full day to schedule in somewhere, and some daytime hours at Epcot. We always get hoppers, so we never have to choose one day to be just one thing, although we will do that with MK on the party night. It will be MK all very long day.
Our departure day is always Disney Springs, and the night before that we will definitely be in Epcot, so that can't be our HS day.
We basically write down how we want to visit the parks in terms of chunks of time and start shuffling until it seems right. But we're flexible, so things can change when we actually get started on the trip, LOL!