Even though it won't be as crowded when you are there in September as other times, you definitely should book the fast passes- 60 days prior if you are staying on property or 30 days prior if you are staying off property. You have to have your ticket number or your resort reservation in your My Disney Experience app to book your fast passes.
It is usually better to book FP+ after the first 2 1/2 hours during which the park is open. You can book 3 FP+ for one park each day, then after you have used those, you can book another FP+ at any park you want, then immediately after you scan that one, you can book another one, and so on and so forth. We took two 18 years with us in May and booked our FP+ for immediately after lunch since they were late risers. Normally, we book them between 11:00 a.m. and 2:00 p.m., then try to get another FP+ for after dinner. However, sometimes you don't have a choice of time. Even booking 60 days out, I often don't get the times I want for some of the FP+ choices.
Fast passes are tiered at some of the parks, so you have to be selective about which of the first tier experiences for which you book FP+. At AK, make sure to get FP+s for Killimanjaro Safari, Kali River Rapids, and then you can decide on your third one. We don't usually use one of our first 3 FP+ on Expedition Everest because it has a single rider line. Dinosaur usually has a long wait, so you might want to get a FP+ for that. The safari at dusk is great, and I also liked it after dark, but many people don't. If the new River of Lights show is open when you are there, go see it, but you can miss the Jungle Book show that is happening now if you don't want to wait. The night entertainment in Africa is nicely done.
At Epcot, I would get a FP+ for the new Soaring rather than the Frozen ride if I only had one day at that park. Test Track has single rider, so we usually use that.
At DHS, we always get FP+ for Toy Story and ride Rock n Roller Coaster using single rider. They opened up a third track for Toy Story, so the wait is still long, but not as long.
At Magic Kingdom, the Seven Dwarfs Mine is a must for a FP+ because the lines get ridiculously long. It is a short ride, but it has great theming. For my son and his friend, it was a one and done.
Since you were last there, the hub in front of the castle and the new portion of Fantasyland have opened. The Under the Seas ride is nicely themed, and Minnie and Daisy are dressed as fortune tellers if you are into characters. If possible, you should try and eat the Be Our Guest, but most reservations will be taken by now. However, if you keep checking back, something will open up. I also think Pirates has been updated to add Jack Sparrow. Also, stop at the fire station to get playing cards for Sorcerers of the Kingdom card game at Magic Kingdom. We had fun doing that while we were walking around.