The CMs usually direct wheelchair users to the accessible seats in the back of the theatre. You'll need to tell the CM your daughter needs a seat up front.
I'll include the wheelchair accessible list, too.

I am glad that it's been helpful.
When the map says
ECVs must transfer-it is talking about the 3 wheeled scooters or the chairs Disney rents NOT electric wheelchairs. Here is a list of rides that you can drive your wheelchair directly onto without transferring, sorted by park:
Magic Kingdom---
Buzz Lightyear's Space Ranger Spin: (note-this ride doesn't fit all electric chairs--my standard Invacare Action electric wheelchair didn't fit-and the shooter is hard to reach, especially with contractures)
Stitches Great Escape (note-the bars that come down on the shoulders could be painful, especially if they are drawn up like mine-I havent ridden it-this ride has got a lot of bad reviews)
Many Adventures of Winnie the Pooh (Takes you through several classic scenes-awesome-easy access)
its a small world (easy access)
Liberty Belle Riverboat (Tour around a lake with some props and animatronics-kinda long-chair sits below level of bars, partially blocking view)-fits multiple chairs
Main Street U.S.A.-Railroad-steam train ride (I loved it. Round trip is best, there are scenes along the way.)-fits two chairs
Jungle Cruise (recently converted)
The Magic Carpets of Aladdin (too short for some chairs)
All the Character Greeting Areas and shows are wheelchair accessible. There are always spaces for wheelchairs with seats for family members adjoining
(Storytime with Belle, etc. all children sit on the floor up front)
Swiss Family Treehouse and Tom Sawyer Island are impossible for wheelchairs (you can do a roundtrip on the raft that goes to Tom Sawyer Island)
All night-time shows and parades have special wheelchair viewing areas-ask a CM, they're marked on a map-nighttime shows are my favorite and are well worth the wait
Epcot
Ellens Energy Adventure (easily accessible-cute Jeapordy style beginning that then takes you back in time to Dinosaurs) fits three chairs
Journey Into Your Imagination (easily accessible-really cute/fun ride with a fully accessible interactive special effects playground afterwards)
Living with the Land (informational tour about various climates and agriculture)
El Rio Del Tiempo (accessible-boat ride tour of Mexico)
The Living Seas-Nemo & Turtle Talk!! (all areas accessible, although some areas may have alternate access. At your own pace viewing of a live sea aquarium and the new Crush attraction)
The World Showcase (all areas accessible, although some areas may have alternate access)
Street shows are hard to see unless you arrive a little early to sit in front
All the Character Greeting Areas and shows (including Innoventions) are wheelchair accessible (*note: The Kid cot fun stop crafts will be difficult to do unless you have a tray on your wheelchair because the table and chairs are low and the supplies are scattered)
All night-time shows and parades have special wheelchair viewing areas-ask a CM--- nighttime shows are my favorite and are well worth the wait
MGM Studios
Great Movie Ride (note-this ride doesn't fit all wheelchairs-my standard Invacare action electric wheelchair didn't fit and I had to ride sideways)
All the Character Greeting Areas and shows are wheelchair accessible
MGM has a lot of good shows-especially action/stunts--all with wheelchair seating
All night-time shows and parades have special wheelchair viewing areas-ask a CM-nighttime shows are my favorite and are well worth the wait
Animal Kingdom-
Wildlife Express Train (train that shows you how Disney cares for their animals and takes you to the Conservation Station-may have to back on)
Triceratop Spin (note: I never rode this ride and I am not sure if it accommodates electric wheelchairs or just manual ones)
Kilimanjaro Safaris (mild thrill ride with a guide that drives you through authentic habitats to view real exotic animals-best experienced in the morning. Note: This ride is bumpy. You may need to back in to the ride vehicle.)
All the Character Greeting Areas and shows are wheelchair accessible (*only parts of the Boneyard. *Conservation is listed as accessible but I didnt visit it.)
All the nature trails are accessible and have beautiful wildlife. There are many exhibits-a few viewing areas are a little difficult to get to.
The parade has a special wheelchair viewing areas-ask a CM
There are plenty of wheelchair accessible rides and awesome shows. Always carefully weigh out the risks of transferring.
Remember all shows are wheelchair accessible-don't miss the nighttime shows-especially Fantasmic-and don't miss Festival of the Lion King where wheelchair seats have prime views.
If there is anyway your daughters can transfer, I would do it for Soarin in Epcot. The ride is awesome. I cannot sit up without complete support and still was able to do it. You can pull your chair right up to the seat to transfer and the movements of the ride are smooth. My Dad sat on one side holding one arm with his other arm around my back/neck and my grandma sat on the other side and held my other arm...
Have a great trip!
Christamae