Yin yang yoga is a form of yoga that aims to combine passive and active asanas (poses), with pranayama (breathwork) and meditation in order to achieve an integrated and satisfying yoga practice.  Yin yoga consists of passive poses that are held for a long time.  These poses target the meridian system and the connective tissues.  Yang yoga is a Vinyasa practice, a type of yoga that moves from pose to pose with the breath.  In yin yang yoga, the sessions begins with a yin practice, moving into a yang or Vinyasa practice, and then ending with sitting meditation.

How Yin Yoga and Yang Yoga Work Together

Yin yoga works by using long, passive holds to work on the deeper connective tissues of the body such as the tendons, ligaments, and cartilage.  These tissues are difficult to energise and open fully.  However, yin yoga is most effective when it is practiced before the more active asana practices (the yang form of yoga).  This is because when the body is being worked actively, the energy flow and circulation is directed into the muscles and superficial connective tissue.
It does not go deeper.

If the passive poses are practiced before the muscles are warm, the energy is able to reach the deeper connective tissues and the corresponding pathways of the meridian system or energy channels.  The prana or life force energy is then able to stimulate and tone the deeper connective tissues, and increase the supply of fluid, thus enabling them to stretch more appropriately.  As a result, the body becomes more flexible, and energy blocks along the meridians are removed, allowing the organs to function better.  The person also becomes calmer and more focused.

Essentially, if you never practice yin yoga in order to go into the deeper connective tissue, it will become less flexible and make it harder to practice the standard yoga asanas.  It also makes it more uncomfortable to sit in meditation.