We recently used a GAC in January, when the lines were longer and had roofs. The CMs are VERY accommodating. I assume that it is a little more "obvious" during busy times, but for us, it was fairly smooth. In January, unless the ride is one of the busier fastpass attractions, we could walk right on the regular line. Otherwise, the fastpass line is easy and discreet.
In our case, my son's autism can be very apparent, so I took him into City Hall, said I needed a Guest Assistance card for him, and the CM knew exactly what I needed just by looking at him. Made it all very comfortable. Just remember to ask questions if you're not sure. We weren't sure how to use it and missed out on a few experiences because we didn't know exactly what to do. Just show the card to the CM at the show or attraction, and they'll tell you what to do.
In our case, we also wanted to sit near an exit in noisy or dark shows, and they didn't even ask us for proof of why.
Disney is wonderful for kids with autism - here's wishing that you'll have a magical time!!