So the shoulders move with the hips, the elbows with the knees, the hands with the feet.
That isn't the complete story, however. These three groups of two (hips/shoulders, elbows/knees, hands/feet) make up the THREE EXTERNAL HARMONIES.
The other three harmonies that make up the six harmonies would include Yi (Mind/Intent, which is frequently paired with "Shen" or Spirit), Chi (Energy), and Li (Strength, pronounced "Lee"). These are known as the Three Internal Harmonies.
You must have a strong spirit ("Shen") in order to do the internal arts properly, and in a self-defense situation to do effective techniques. Your mind and intention must be clear, determined, and focused (Shen and Yi), your body mechanics and technique must be good (Chi), and then your strength will be powerful (Li). All three of these must act in harmony.
Let's go back to the original list of six above (the Three External Harmonies). For these parts to move in harmony, there must be a connection. So if you're doing any particular movement, your feet are connected through the hands, your hips through the shoulders, and your knees through the elbows.
This is another way of talking about whole-body movement and silk-reeling. Each part can move separately -- on it's own -- and yet the movement is not effective and not internal if the other parts are not moving in harmony. A strike with the hand must also use the feet (ground) and it spirals up through the knees, waist (dan t'ien), shoulders, and elbows. Silk-Reeling movement -- spiraling -- must happen throughout, and the ground path and peng jin must be maintained along with proper structure. That is how you establish "chi flow."
Think about this the next time you're practicing a movement -- use Buddha's Warrior or Lazy about Tying the Coat. You notice that at the beginning of Lazy About Tying the Coat, you step out with your right leg but your right elbow isn't really over the knee and the right hand isn't over the foot, so the idea that the elbow must be over the knee or the hand over the foot isn't really accurate.
However, when you are doing the movement, you are connected if you perform the movement properly. Even at the end of the movement when you are "relaxing," your elbow is spiraling as you sink and your entire body should be closing. At this point also, your elbow is over the knee and the hand is over the foot.
Where does the breath come in? It is coordinated through your movements. When practicing a form, you should breathe naturally. But in self-defense, when executing a "yang" or attacking technique, you should exhale, coordinating your spirit and your breath (and body mechanics). When you do that, your strength (Li) will be evident.
Spirit can also be described as "attitude." If you are mentally frightened or insecure, your Spirit (Shen) is unable to support a strong Intent for your mind (Yi). When someone attacks you and your Shen is weak, you might cover and be unable to defend yourself. But if your Shen is strong, and you put your mind into the task at hand and you are determined to defend yourself and fight ferociously, you then have the Shen that you need. At that point, your Mind/Intent (Yi) is determined to defend yourself. You are mentally strong and you will not accept the idea of defeat. Next, if you have trained your body to respond with proper mechanics, technique and breathing, you can support your strong Spirit and your determined Mind/Intent with strong Chi. The result will be strong Li (Strength).
If any one of the first two Internal Harmonies is not present, your Strength will suffer. If you have strong Spirit/Mind/Intent and Chi, your Strength will be there.
This is how you translate Chi from a mystical perspective into a more realistic perspective. This is what Chi means from a martial perspective. It is NOT a literal "energy" running through your body along meridians. It is the manifestation of proper attitude and body mechanics.
You can find more video lessons on the Six Harmonies on the online school.