I noticed when doing these tutorials again after I applied automatic weights that the rig would move differently from what you had. I went back to this lesson and realized that the parenting changed in the shoulder bone but wasn't referenced in the video. There is a transition cut in the video from timecode 6:58-7:00. Where you see that change. Am I supposed to parent the shoulder to the Neck now? I tried making this change but now my rig doesn't move correctly at all.
Hi Xavier,
The relationship lines run to the tail of the bone (by default). So that dotted line actually runs to the Chest.
When I duplicated the Chest bone to create the Shoulder it copies the parenting (Spine_02).
But later in the course when it comes time to building the control rig the parenting will be finalised. A simple way to think about it is that every part should flow to 1 bone inside that component, and then that one bone is connected to the part higher in the hierarchy. (of course that's not always possible but it's a great way to simplify your thinking)
Later that shoulder will become the DEF-Shoulder.L and be parented to the Shoulder.L.
The Shoulder.L will be parented to the Chest_02_tweak.L
If it doesn't make sense now Xavier, don't worry it will ;)
Yeah still a bit confused. So Right now my rig is like this. Is this ok? 
When I move the chest bone it deforms like this where the arms dont move with it. Compared to the one you have where the arms move when you move your bone. Is there something I'm missing?
That looks pretty close Xavier.
I can see that the shoulders are parented to the Spine_02 though and not the Chest. That's why the shoulders are staying put when you rotate the chest.
But as I said, when you build the control rig all the parenting should be sorted out and corrected (if it needs adjusting)