Currently in flash builder I group my code into "Groups", but I just found that I can't apply transitions to them so they move or fade their content during a state change.
Is there a container that I can apply transitions to?
There's no special restriction on Groups; you should be able to Fade/Move/whatever on either the group itself or its contents. If you post a small app I can take a look and see what's going wrong.
You are right, the problem I had was that I was not setting the group's id, I was changing it's "d:id", so I saw no effect.