If you follow the link in my signature to the disABILITIES FAQs thread, one of the posts in that thread is all about air travel with a wheelchair.
What you want to do is gate check the wheelchair and I would suggest mentioning it when you fist check in for your flight. They may give you a gate check tag right then, or tell you to check at the departure gate. If at the gate, don't wait until they have started loading, do it as soon as possible after the gate agent opens up the desk.
When you gate check a wheelchair, you can choose whether to get it back at the end of your flight or at an in-between airport for a transfer. They can do it either way, but if you have a layover, it's important to make sure you have enough time between flights to actually get the wheelchair delivered to the gate. Sometimes a tight connection means you won't have time to get the chair delivered and make your next flight.
You MAY be able to store the wheelchair in an on-plane closet. If you want to do that, mention as soon as you check in because they are required to have room for only one wheelchair and it is first come, first serve (if they have a closet at all - some flights don't).
Most airlines do not automatically preboard people using wheelchairs. They used to, but most do it on request now, rather than routinely doing it.
There is a lot more information on the disABILITIES Board about travel to WDW with a wheelchair - there is a lot in the disABILITIES FAQs thread and you can always ask questions.
For attractions, she will be able to stay in the wheelchair until boarding the ride car and some ride cars are actually wheelchair accessible. Shows have wheelchair accessible seating areas where she can stay in the wheelchair for the show. At AK and the Studio, the 'regular' lines are all wheelchair accessible (these are called Mainstream Lines). Most of the attractions at Epcot and MK also have Mainstream Lines, although some are not accessible because of the age of the park. For those non-accessible lines, there will be another way you can access.