God is everywhere in His fullness. His fullness is not contained only by the sum of every part of the universe, but it found in the tiniest part, if I can speak of God in such metaphysical terms. So the fullness of God could dwell in Jesus bodily and still have God exist apart from the incarnation. An analogy would be helpful here. This phenomenon could be compared to a balloon and air.
Air permeates our atmosphere.
This is likened to the Spirit of God who is invisible and omnipresent. Jesus is likened to the balloon that is filled with air. The balloon is the incarnation of the air. Just as the air in the balloon is no different than the air that is outside of the balloon, even so the deity in the man Christ Jesus is the same deity that exists as the omnipresent Spirit. Likewise, just as the air that is in the balloon continues to also exist outside of the balloon, so likewise the Spirit of God continues to exist apart from the incarnation as the omnipresent Spirit.