I have never had a problem with my wheelchair but I always bring mine through the lines with me. I suggest you do the same - you never know when the ride will break or the line slows down, and you get stuck longer than your son wants to/can stand. You can have him stand up as soon as you are in the line, or even before - I have seen people pushing empty wheelchairs into queues before (generally not empty park rentals, but those too!). This will allow CMs to guide you around stairs, which may be a difficulty for him (especially since sometimes you have to wait ON a stair and not just climb it).
My wheelchair is generally parked within a few feet of a CM at all times - even when I could walk, I always brought it into the lines with me. It also gives me the option of using a wheelchair boat/vehicle, which may be easier for him than transferring (or just plain cool - he gets to sit higher than everyone else on Jungle Cruise and Small World, and that is just off the top of my head).
Sometimes the wheelchair car may offer a more secure seat for him than transferring - I am thinking of Buzz Lightyear and especially Toy Story - he is less likely to slide out of his wheelchair than one of those short depth hard plastic benches.
I am not sure what his disability is, but I can only transfer a few times a day mostly because my tush can only handle sitting on hard plastic a few times a day. I cannot decide if it is a good thing I have decent sensation in my rump so I know when to move around to avoid pressure sores, or a bad thing because those hard plastic seats make my rear end sore!
I know he may prefer transferring for shows, so he is not in the back row, especially if his chair is very low to the ground (not sure of his age or size), but for Monsters Inc Laugh Floor, definitely have him stay in his chair - not only are there wheelchair spots in the middle, but the seats are the least comfortable things I have ever sat on!
For some rides when I transfer, and it is permitted, I bring my seat cushion - my tush thanks me.
For American Adventure, definitely transfer - only one person can sit with him and the view kinda stinks. You will have to ask where to leave the wheelchair to get it after the show. I would not leave it outside, which is what they ask people to do if they do not plan on taking the chair into the show - you can be in the building over an hour and you never know when it is going to rain in Florida!
That is my number one reason for suggesting to ALWAYS bring the wheelchair into the queues with you, even if he walks to avoid stiffness (or just because he wants to) - you do NOT want a custom chair out in a downpour!
Also, not sure if you have had to do this before, or if he was in special needs strollers (or regular strollers) before this, but for me and my chair, I use a double poncho system - I put one over the chair any time I leave it outside even for a second, or of I know the CMs need to move it (like at BTMRR). If it starts to rain, I cover the chair itself with a poncho and then wear one myself. I know I will not be pushing myself much when it rains - very hard to keep handrims at all dry), so I am mostly trying to keep the cushions (and me) dry.
Even during "dry" seasons, I have been caught out in the rain, so I always bring ponchos with me - I get mine at the Dollar Tree (usually a 2 pack for $1). They are cheap, no doubt, but when it stops raining, I just throw them away rather than try to carry a wet thing. Also, they come folded as small as a men's wallet, so easy to bring with you.
When it comes to keeping track of the chair - Never lock it to a railing or post. Security WILL cut it free if they have to. You CAN lock one of the big wheels to the other or to the frame (what type of chair does he have). Most custom chairs are light enough CMs who need to move them do not even try to take off the brakes (unless they need to move it long distances like BTMRR) - they just lift up on push handles and wheel it on the casters.
There are devices that can be found in wrist bands and such that are used to locate children with autism or other disorders who are elopers, but you probably do not want to carry the track equipment with you.
My biggest suggestion is just to take the chair into queues with you, even if your son walks. This will keep the chair out of the elements, out of stroller parking (where CMs may need to move it and kids may mess with it) and close to where CMs stand.
My last suggestion is that whenever I leave my powerchair for any length of time I disconnect the battery. Whenever I leave my manual chair, if I can, I fold down the backrest - this also helps discourage people from sitting in it. That is much more likely than theft - just a kid thinking it looks cool to sit in (this usually results in peanut butter fingerprints more often than damage).
Sorry this was so long. Hope some of it helps!
