I know there is someone on this board who has done it...I remember reading about it. I wish I could remember who and point you in her direction.
Anyway, if I recall correctly, I think what she did was have velcro openings in the back where she placed rows of (whatever the weighted pouches were). The weighted pouches were removable for washing.
I would probably want to quilt the whole thing, then add the pouches on the back. If you did it in rows instead of individual "bean bag" sized pouches, adding the required fabric shouldn't take too much work.
For the pouches, I think I would sew long rows (the width of the quilt) to contain whatever you're using to weight it, and then sew lines across to evenly distribute the weighted material to keep it from shifting within the larger row sized pouch.
I would use a light weight velcro, only because kids with Autism can have textile sensitivities and I wouldn't want the coarse velcro to cause problems with that...I wonder if you could use those metal snap things instead of velcro...? Might irritate sensitivities less.
Hm. I've never made one of these, and I don't know if my ideas would really work. I'm just kind of typing as I think. I hope some of my thoughts will help you in your process. :o)