You either love EMH or you don’t.
I personally love EMH and almost always take advantage of early EMH. At the most crowded times of the year, I’d get nothing done if it weren’t for EMH. For example, we were there this past year for New Year’s. On December 30, we went into MK at 11:00 that night, watched the fireworks. The rest of the park cleared out after the fireworks, but we stayed for evening EMH and hit all of the big attractions with little or no wait. The park wasn’t crowded at all.
Now, EMH is also a hit or miss. A few years ago (4th of July), we got to AK after EMH had already begun, and even though the park hadn’t officially opened, yet, it was already packed. Of course, we did the same thing, last weekend for Epcot, and the wait times were still low. It depends on what time of the year you’re going and what the crowds are like.
September is fairly uncrowded. We went last year for Labor Day and EMH worked great. We went into the park for EMH, then went to our breakfast reservations for later that morning. I suggest planning a late breakfast (10-11am) so you can tour the parks with minimal crowds, first. You definitely don’t want to have an 8:00 am breakfast ADR if EMH starts at 8:00 am that morning.
Are you getting park hopper tickets? If so, then you have little to worry about. If you get into the park and it gets crowded, leave. If you don’t have PH tickets, plan to take a resort break from noon-3 when the parks are the most crowded.
I think you’ll be fine. September usually isn’t that crowded, anyway, and EMH can very well work in your advantage. Just make sure that you wake up early and get to the parks BEFORE EMH begins that morning.