How a Guest Assistance Card is handled depends on what accommodations are needed. The line is indoors and air conditioned and most of both the regular and Fastpass line are accessible.
How the accessible boarding area works is always the same. There are no seats in the accessible boarding area - it is just a line with wall on one side and a metal rail on the other side. It can sometimes be very busy and tight, depending on the number of people waiting.
For guest's who need to wait away from other other guests, there is a small room just past the exit. I have never actually seen it in use, but have been told guests would wait there equal to the expected wait time and then go from there to board. That room is visible from the ramp when exiting the ride - its just a room, no seats or anything.
The regular line and the Fastpass line do not have any stairs until the point where they merge. This is just after the 3 D glasses pickup point and just after Fastpasses are collected. At that point, there is a set of stairs to the left and a ramp to the right.
Guests who can't do stairs are sent to the ramp where there is a waiting area for those guests.
That boarding area has a section of track where a ride car 'pod' can be diverted from the regular track. They open a switch, the track moves slightly and the ride cars go into the accessible boarding area. Then the track is switched again so no more ride cars are sent to that section if track. After unloading /loading, the track is switched again to let the ride cars leave the area and get onto the main track.
The stairs in the main line actually go up to go over the portion of the track that is diverted to send ride car pods to the the accessible area. After crossing the track, the stairs go down to get to the regular boarding area.
There are some links in post 3 of the disABILITIES FAQs thread that show the ride queue, including the stairs - its just above the information about Disney Quest in that thread.
There is a wheelchair accessible ride car that is sent to that area. The 'regular' ride car pods contain 2 ride cars that each have seats for 4; so the entire pod holds 8.
The accessible pod has one car that holds 4. The other car holds 2 and has the ability to be converted for wheelchair access by folding down the back of the ride car to become a ramp. The 2nd seat is removed to become a wheelchair spot.
Guests who can transfer would usually wait for that pod to come around and ride in that pod. If they have a wheelchair,
ECV or other mobility device, it will be waiting at the same place they left it when they return.
Sometimes, a regular ride car pod will be diverted to that boarding area for those guests who can transfer. In that case, their mobility device will be pulled forward into the regular load/unload area where they will get out when the ride is done.
CMs have told us that they are supposed to use only the accessible car, but can pull one 'regular' car pod into the area for loading each time they need to convert the car for wheelchair use. This is because it takes several minutes to covert the car, load the chair and then reverse the process to unload.
There are no seats in the accessible waiting area and the wait can sometimes be quite long there - we have already waited for 35 minutes just in that area. Depending on the number of people waiting, much of the wait could possibly be in the ramped area that leads into the accessible area. The reason for the long wait is that anyone who needs to avoid stairs for any reason needs to use that area.
If you can do stairs, your wait will be shorter continuing into the regular boarding area using the stairs. The times we have been in larger parties and had to divide up, those who used the stairs have usually been done and exiting the ride while DD with a wheelchair and the rest of the party in the accessible area were still waiting. So, using the accessible area will not shorten the wait and may make it longer, whether or not the accessible car is needed.