Sorry if I made it sound complicated. The pass really isn't complicated but as I pointed out they are not meant to shorten wait times. They are meant to provide you service to meet your needs so waiting in a quieter place or in an area with less stimulation. They also are not suppose to work like fast passes.
If the wait is the big issue then fast passes are the best option especially if using and iPod or other device to keep him focused on something besides the noise of the parks works to keep melt downs at bay.
The most important thing is to have a plan for the what ifs. Even with a GAC melt downs are possible so knowing what you are going to do if one happens is the best plan.
First aid and Baby Care are your friends. If he needs to rest and get out of the stimulating environment instead if going to the hotel you can go to baby care or even first aid. Just let them know you just need a quite moment to help reset and then you'll be about your day. Each park has one and the staff has always been super friendly when ever I go in.
Don't be sorry, you have been extremely helpful! First aid and baby care are great alternatives that I didn't even know that was an option, thanks! Fast passes work great for us, the only place my son had a meltdown was in the line waiting to see a show at Hollywood studios. It was just too hot and there were too many people. We probably won't need the gac at all but it's nice to know that it's available. Thanks again!