As long as it is in the Disney Resort area they don't care which hotel you drop off at and pick up from.
However, to avoid confusion just ask for a Roundtrip ticket to the hotel you are being dropped off at.
The day before your pickup, go to any Disney House phone (or your room phone) and dial "0".
Ask to be connected to Mears, then tell them where you need to be picked up from and what time your flight is and how many in your party and they will give you a pickup time.
You can book in advance online, but they charge your credit card right then. If you have one of the $3 coupons you can't use it unless you purchase a ticket at the counter.
In September, I bought a round trip ticket for my son because he was going home by himself for the school week. Only spending the weekends with us.
I told them I needed a round trip ticket from/to the All-Star Movies. (That is where we were staying)
He was picked up at Animal Kingdom Lodge (no luggage, and we were at Animal Kingdom when he had to leave) and returned to the Beach Club. (We were eating dinner there when he got back)
Even though he was going the opposite direction on his ticket and totally different resorts, noone even blinked an eye.
Carol