There are separate boarding lanes for guests with mobility devices at each station.
At the Studio and EPCOT, there will be a CM directing. The line for mobility device boarding is at the left side of the station and is marked with a wheelchair symbol.
Caribbean Beach is the transfer hub where guests transfer from one Skyway line to the other. There will be a CM sort of in the middle of the station answering questions and directing guests. They will direct you or look for the wheelchair symbol.