Here are a few more of Frank Thomas' rough character layouts for the second half of the scene. The sketch above establishes the size relationship between Hook and Smee.
Hook anticipates a reach toward the bewildered Smee.
He then extends his arm to get a hold of Smee.
Hook reacts to the crows nest announcement that Peter Pan is approaching.
His attention now lees with Smee, instead he is processing what he just heard.
He then drops Smee , turns toward the crows nest to give an order.
All this is so carefully staged and timed out in the animation, that you are never in doubt about what the characters are thinking.