Hi Tomiko!
September is a relatively quiet time at Walt Disney World Resort so I wouldn't worry about the crowds so much when you figure out your itinerary. I recommend planning on spending one full day in the Magic Kingdom, one full day in Epcot, and one full day in the Studios. I also recommend spending one full day at Animal Kingdom, because I love that park, but many guests consider Animal Kingdom to be a half day park.
You didn't say exactly when you are coming so I hesitate to put together a detailed itinerary. However, you can look at the Walt Disney World Resort park calendars on the main website to see when each park is offering morning and evening Extra Magic Hours. Just click
here. Then under "Parks", click on an individual park such as the Magic Kingdom, then click on calendar. You can then see the hours, and any special events, for each day of the month!
With regards to dining, definitely make Advanced Dining Reservations before coming. My family loves Tusker House in the Animal Kingdom, the Whispering Canyon Cafe in the Wilderness Lodge, the Sci Fi Theater in Disney's Hollywood Studios, and Liberty Tree Tavern in the Magic Kingdom. We also love Boma in the Animal Kingdom Lodge and Cape May Cafe at the Beach Club.
Enjoy planning and write back if you have any more questions!