So how do the muscles, tendons and ligaments know what I want them to do?

Let us assume that you want to scratch your ear. Your brain cells send a message through your spinal cord and motor nerves to the muscle cells that need to be activated. The muscles that bend your elbow are told to contract. Then the information returns to the brain from the muscles and joints, so as to regulate the amount of strength or force that is needed to bring your hand up to your ear. Then additional messages are sent to the muscles that will control how the fingers need to respond and what action they need to take.
Now you are able to apply the exact movement and pressure required. If the system was not so exact, you could give yourself a black eye!