Here's a
link to the official WDW site's disability page. It includes a link for the Guidebook for Guests with Disabilities for each park. You will notice that most attractions have what they call "Mainstream queues." That means that the queues are wide enough to accomidate wheelchairs and
ecvs. For those atractions, you will be using the standby lines unless you have fastpasses (so, yes, as Lindsay noted, you should get fastpasses).
For most shows, you will enter in the regular entrance and then be directed to the back of the theater where there are spaces for wheelchairs. Some shows, like Beauty and the Beast and the Indiana Jones Stunt Show, have seating in the front and the back. Be there early if you want to get the front seats.
For Fantasmic, we have gotten there as late as 15 minutes before the show (during Spring break, no less) and still gotten space. I would suggest getting there 1 to 1.5 hours early though. The wait is not really as bad as it sounds; you are seated, there is a snack bar and bathrooms in the area if you need them. We are usually surprised how quickly the time goes. The closer to the show start time you wait to go in, the busier it is and the more difficult it becomes to drive thru the crowds.
In most attractions, the CMs do a good job of letting you know where to go, what to do.
Check out the
disABILITIES FAQs thread for more info.