Hi Veronica,
Sounds like you're planning an action packed vacation - love that!!
With the Park Hopper Option, you are able to visit all four of the theme parks (Magic Kingdom, Epcot, Disney's Hollywood Studios and Disney's Animal Kingdom) as much as you'd like in one day. This incredible flexibility allows you to have breakfast in one park, head to another to ride your favorite attractions and watch fireworks at another park in the evening.
Usually the crowds are lower towards the end of September and its a good time to visit. There are a few things that may impact that week.
Mickey's Not-So-Scary Halloween Party is being held at the Magic Kingdom on the following dates in Sept: 13th, 16th, 20th, 23rd, 27th & 30th.
Epcot's International Food & Wine Festival begins on September 30th so that may start bringing some people in towards the end of your visit.
October 1st is Walt Disney World's 40th Anniversary and may be a big draw for Guests to visit the Magic Kingdom on that day. I know I want to be there for sure.
Wishing you minnie magical memories :-) Allison