Wow, it is kind of hard to describe exactly where their ears are. I even took a long look at Mimi's head to see if there were something that I could use to describe their location, but her ear coverts don't look any different than the rest of the feathers on the sides of her head, but they will be almost directly behind her eyes maybe a quarter of an inch and perhaps just a little lower. Still their ears are internal with just a hole at the surface of the skin, so it is very doubtful that you can hurt them with the amount of pressure that the bird will allow when you rub or scratch his head.
As for the head bobbing thing, there could be a variety of reasons one of which is simply rearranging food in the crop. Another possibility is that it is a hormonal response. Kookooloo, my Grey is in her second breeding cycle and she does this on a regular basis , but she also does it when she is happy and pleased with herself ot in greeting to me, so these are also possibilities. Since Amazons should not be in breeding mode, I would guess that it is a pleased or happy reaction to your presence.