FlyingPenguin always gate checks her manual chair and gives them the power chair (if we take it) at checkin. (So many places/vehicles which won't take a power chair that she takes both. Much easier for both airport and us to get the power chair and all its paperwork dealt with early.)
We've been pretty unimpressed with Alaska and America West. United and American have both been good. This is out of SEA and, obviously, airline staff differ a lot from airport to airport. (UA staff in ORD, for example, are very officious.) To give a specific example, her power chair with back upright won't fit through the cargo doors of an MD80. Alaska handled that situation by putting the wheelchair on its side and, inevitably, breaking one of the control boxes. Later when we were on an American MD80 flight, we queried them about the size and they said we'd need to remove the back from the chair, and staff member said they would put the wheelchair on another plane if it wouldn't fit safely upright. He then went down to the plane to check and came back to us at the gate to tell us that it make it with less than an inch to spare. Alaska staff have also tended to want to push the manual chair and have even started to do so without asking!
So long as the chair/scooter fits into the hold, they won't do any disassembly. Hold doors are tiny on 737-200s and MD80s, so best to avoid them if you can (as if most of us don't already!) when taking such a large object. Airlines are paranoid about batteries. If you don't have an obvious quick disconnect cable that totally removes any chance of power being applied to the motor or controls, they will want to take the batteries out and physically disconnect the terminals (and cover them in tape). If you do have such a cable, they will just cover the ends of the disconnected cable with tape.