Andrea:
You'll find three modes of transportation that you may encounter on your trip at Disney: buses, monorail and water ferries. My dad is a paraplegic and was pleasantly surprised by
how accessibility Disney transportation is. There is only one bus stop at Pop Century and it is at the front of the resort. If you have a reserved a Preferred room you should be close, but I would suggest making a note on your reservation that you'd like to be near the bus stop for your daughter who is in a wheelchair. All buses are equipped with either a portable ramp or what I call "kneeling" capabilities for wheeling on with a ramp. On most buses, you'll find clamps for up to two wheelchairs along with secure fasteners. Although it didn't matter to my dad who is used to traveling on his own, the seat for the wheelchair user's companion is not directly beside the wheelchair area but across. We did not find a single instance when a bus driver was not cheerful or fully accommodating.
As for the monorail, you'll be able to wheel on after a cast member puts a portable ramp up to the vehicle. Most of the ferries will not require this, including the boats in Epcot. You should be able to wheel straight on. The small boat launches, however, that move between the Magic Kingdom resorts are not wheelchair accessible and would require your daughter to exit the wheelchair before boarding. The likelihood of you having to use one, though, doesn't sound likely, though.
If you have any more mobility questions, please feel free to come back and ask!
Wishing y'all a magical vacation!
Whitney