My husband and I took our then 3 1/2 y/o GS to WDW last Feb (2012). We talked to him before the trip about how Nana would go through the metal detector first, then he'd follow, then Bopop would come right behind him. When we got to security, we were pulled over to the full body scanner.

As we got into line, I started explaining how I'd go through, the doors would close, then I would have to put my feet on the yellow footprints inside, and would have to raise my arms up and stand really still while they took a picture, then the door on the other side would open, I'd walk out and then he'd have to do the same thing. He is very tiny for his age and looked maybe 2 y/o, but is also very smart, so was just nodding that he understood and would do it, but also looked rather tentative and nervous as he held my hand. The gate agent over there, shook his head, glared at his coworker who had pulled us out of the other line and told my husband to take our GS and go back through the other line with the regular metal detector. I asked if I could go with them, but he said no, one of us had to go through the scanner, but there was no use putting our GS through that, so he was sending him and my husband through the regular metal detector. My husband sent him through first, telling him to wait for him on the other side. My GS did fine, but really was not happy that I was seperated from them, even though he could still see me. I'm still not sure why I got called out for the body scanner. I was wearing shorts and a thin tshirt, so obviously was not able to hide anything, even if I'd wanted to. Anyway, my point is, you might want to prepare them that one of you might get pulled to another area to go through a different scanner, so you might get seperated, but that's OK and not a big deal.
Oh yeah, if they have any kind of stuffed animal with them, let them know ahead of time that they will have to let it go long enough to go through the scanner with the carry ons. The first time, I took my GD on a trip she had a little stuffed green bunny that she took everywhere and was very unhappy when she had to put it on the belt to go through the scanner. That was my fault for not preparing her.