All five of us will be heading to our happy place in June! This is our first time to fly on SW. I incorrectly thought that at the 24 hour check-in point I would be able to make actual seat assignments like on AirTran. I now know that it's just a boarding order. I'll do the check-in as early as possible and hopefully head off any problems, however I want to have my bases covered. DS HAS to sit beside me on the flight or we might end up kicked off the flight.

(We also have DDs age 5 & 8 that I'm not keen on having sit with strangers, but one problem at a time.) Is there some way that I can ensure that DS and I will be seated together? Should I have a doctor's note? Just let them know at the boarding gate? Something else? It's not as if they can "see" his disability. Experiences anyone?
I always fly SW to Orlando and here's my experience. I get online a few minutes before the 24hr check-in time and have my confirmation code already entered on the website. Then when it's right at the 24 hour mark, I hit the enter button. Sometimes it'll tell me that I'm too early and I just keep repeating until it lets me check in. Every single time I've done this, I've gotten boarding group A. In boarding group A, you're pretty much guaranteed of getting seats together.
The day before leaving WDW, go to the concierge desk around 24.5 hours before take-off time. The concierge will do the check in for you as long as you have your confirmation number. I said 24.5 hours because that gives you time to allow for lines. Bring your refillable mug (I love those) so that if there's no line you can take a detour to get a drink to kill that half hour.
Last time we were at WDW, we couldn't get back to the hotel in time to do the 24hr pre-checkin. We checked in around 20 hours before. We got boarding positions B1 - B4. Even with the family boarding between A and B, we still had no problem getting seats together, and there were still plenty of empty rows left. This is on a flight that was so full that they asked for volunteers to get bumped to another flight.
On this same flight, there was a mom with a daughter who suffers from epilepsy. She said she had to sit beside her daughter just in case of a seizure. She was one of the last to board and started yelling at a flight attendant how she had to sit with her daughter for medical reasons and how the flight attendant HAD to figure something out and how she had a doctor's letter stating this. For the life of me I can't imagine why this woman didn't make sure to get an earlier boarding spot (uh, it's her responsibility to get checked in earlier if she knows she has a special need; that's what you're doing and that's what the rest of us with special needs do, we take personal responsibility). There was a very nice woman who changed seats so they could sit together which was great for the daughter, but the mom made me mad. Sorry for venting. People like you go out of your way to do the right thing and then you see people like that woman and they give all of us parents of special needs kids a bad name. I guess my point in this vent is to say that even if you don't immediately find seats together, there are wonderful people who will swap seats for people who need it. The world really does have a lot fo wonderful people in it.
If you don't get boarding group A, I would discuss the issue with the person at the gate when you arrive. They don't want a child who will be upset or disruptive on a flight any more than you do (for them it's a safety issue). I would imagine that they would let you pre-board or board with the families with small children in order to guarantee that you sit together. If you're in boarding group A then I wouldn't even worry about it. Then again, if he'll have trouble with the boarding procedures with others boarding at the same time then you might want to consider asking about pre-boarding for medical reasons. Boarding with group A might be easier if you go straight towards the back of the plane so that there aren't as many people moving around you while you're settling into your seats.