What is the difference between primary and secondary raynaud's syndrome?

Depends on the cause. When a patient has raynaud's phenomenon (vasospasm leading to poor circulation in the fingers and toes), his doctors will look for the common causes such as autoimmune disorders, drug side effects, hormonal imbalances, etc... If no medical condition is found that is causing the symptoms, then the disorder is called "primary". If a condition is found, then the disorder is "secondary".
Primary has no cause. Primary raynaud's has no known cause, just symptoms. Secondary raynaud's is symptoms that are a part of another diagnosis such as thoracic outlet syndrome.