Call the airline a day or so before your trip to make sure that you get wheelchair assistance. If possible, ask for the contractors phone #, so you can call and arrange with them how they pick you up from the taxi. They can probably help you check in.
I guess its different from airport to airport, but you can usually keep the chair while youre waiting. With regards to help from FAs and stowing, yes.
If your assistance need is proper booked by the airline, it should not be a problem at your stopover, theyll meet you right outside the airplane. Im assuming you can walk a short distance, so your "code" would be WCHR, which pretty much is all wheelchairs users who can walk a little by their selves, with crutches too. If you cant walk stairs, ask the airline to put it in as a WCHS. But I assume the plane is going to park at a jetway, and it wont be a problem.
Again, different from airport to airport, at my airport, youll get help out to your taxi with your luggage. However, I believe the "airline's responsibilty" stops at the conveyor belt... Here, the airport has a contract with the wheelchair contractor so people get help all the way out to their taxi/train/rental car. If not, you could probably find some kind of a porter service that could help you with the luggage..