I'm afraid I've not read all the replies (my brain's pretty foggy today), so I may repeat what people have already said. So, here's my 2 cents (30 more and I could get an airfare

):
For restrooms, I would suggest using the companion restrooms or the first aid centres. These are larger bathrooms, designed for those who need assistance or extra space due to their disability. They aren't marked on the regular maps, but they are on the parks disabilities guide (available at Guest Relations).
Staying on site would be a good idea, as the transport makes it so much easier. I think all of the moderates are lovely. They're clean, well designed, and not too over stimulating. POFQ is a relatively small resort, meaning that you don't have to go so far to get anywhere, but on the downside, there is only one pool. The others are larger, meaning further to walk (though you could request a close room for medical reasons) but more pools. If he likes exploring, CBR might be a good one, as it has a whole island with a playground and parrots, as well as beaches all around the resort. If he's a bolter, this may not be so good.
Just to warn you CSR has a weird system at their food court; it might work for you, it might not. You wait to be seated, the server takes your drinks order, then you go up to the food court counters to choose your meal (as with a normal food court). You have to pay at a podum after your meal. They then add 15% service to your
whole bill. You can refuse to pay the service, but that seems like a lot of fuss to me. It seems like a weird mix of the worst bits of CS and TS, but I know some people prefer this system, so it's down to personal taste.
Another option for accommodation, you could look into renting DVC points from an owner over on the DVC boards of this forum. This can allow you to get a studio room with a kitchenette for about the same price as a moderate, so you could have some (simple) meals in the room. They do have larger villas with full kitchens, but these are more expensive. You also get all the normal perks of staying on property: transport, EMH, Disney service etc. Just be aware that there is a bit of a risk involved, as you are renting from an individual, not Disney. However, they've got lots of useful advice available there, and if you follow that and your gut, you should be fine.
Also, if you're flying into MCO, you can use the free Magical Express, which will take some of the cost and hassle out of getting to the resort.
I'm guessing, as you've gone with your son before, that you know about the GAC (if you don't check out the FAQ). Get one, and use it as much as you need to.
Would they both fit in a double stroller? If so, this might conserve his energy, provide a 'safe place', and stop him from bolting. If you do get one, see if you can get a 'stroller as wheelchair' on your GAC.
Only you know how he'd cope at food courts, but a few 'coping strategies' might help you deal a bit better. Try to go for meals during quieter times, to reduce the stress of the crowds; carry some small snacks with you, to help both the kids 'last' between meals, especially if you're eating at different times to normal (might be best not to let them know you have these, though, or they might be clamoring for them!); if he's on any special diet, look though this board for tips on managing allergies / dietary requirements; giving him a 'job' such as carrying the tray, or remembering the order, might help keep him busy.
Some people have found small toys, games consoles or music players with headphones help keep their kids' attention away from the crowds around them and keep them calm. Just make sure he doesn't have them in attractions, or he might miss stuff.
If he needs a rest, or to get away from things, the First Aid centres have beds you can lie down in for a short while.
You're going during what I think is a fairly quiet time, so you shouldn't have too many problems. If you have any trouble, just ask the nearest CM and they'll do what they can to help!
Have a great time!
