I would just bring your single stroller for the baby. We picked up a larger-type stroller at a local thrift shop actually (lucky find!) for $10 and used that for our daughter when we went to Disney last year, when she was 3.5. She wasn't in a stroller any longer at that point but it really came in handy at the park when she was tired and/or we wanted to get someplace quickly and we didn't have to worry about losing her in a crowd. Folding and unfolding it on the trams and monorail was not that big a deal. We donated it back to the thrift store when our vacation was done. I also appreciated having the basket down below for bags and camera. They do have strollers to rent at the parks if your son suddenly seems to need one, but they are around $15 a day.
If you are going to Sept, start getting your son used to lots of walking now. Spend the summer walking longer and longer distances every day to every other day so by the time it is time to go, he will have built up some endurance. When we took my husband's sons to Disney when they were 6 and 7 (and probably barely weighed 50 lb each) they had no problems walking with us - they kept right up and never complained about getting tired (but then they were hungry all the time!). Last month we were at Disneyland in CA - not quite as big, but still a lot of walking. Daughter is now almost 5 and she walked just fine. They have a train that goes around the park with 4 stops so sometimes we used it just to give her a break and make it easier to get to the other side of the park rather than walking more.
Get the Unofficial Guide to Disney World - they come out with a new edition every year and it's always proven to be invaluable to us! Especially when it comes to planning how to hit the rides and do the most while minimizing waiting in line!