ECV's and wheelchairs have a separate loading zone for the Skyliner. I believe you wait in the same line as everyone else until you get to a spot where they will move you to the ECV/wheelchair entrance. (Someone please correct me if this is not right).
When it comes to loading the Skyliner, there are cars that pull onto a separate track and come to a full stop for boarding and disembarking ECV guests and the rest of their party from the cabin. Once loaded your cabin will move back onto the regular cable. With the exception of the Riviera station, all WDW stations have this pull off area.