It is a common misconception that joints can be painful because they are "in the wrong place" and that a manual technique reduces pain by "putting the joint back in place". This is only the case in acute dislocation.
Pain and pain perception is very complex and involves different parts of our brain and nervous systems. Recent scientific evidence shows that manual therapy applied to joints and soft tissues works on two different levels to help reduce pain:
At the level of the spinal cord
Manual techniques stimulate nerve receptors in joints and connective tissue that send messages to the spinal cord, blocking incoming messages to the spinal cord from the painful area.
Within the brain
Manual techniques stimulate the brain regions involved in pain modulation, causing the brain to release its own form of natural painkillers and inhibit incoming messages from the painful area.
This is important to understand. Incorrect beliefs regarding the mechanism of pain can contribute to its long-term maintenance or exacerbation.
Because of the pain reduction you experience as a result of manual therapy, you can move more with less pain and discomfort. It is important that you continue to move and perform the specific exercises given by the therapist to maximise the effects of manual therapy.