the molex connector will power the fan and normally run it at 100%. the mobo header will normally allow for you to control the fans speed and to set a fan curve if you wish through software. though this usually requires the 4 pin connection rather than the older 3 pin mobo connection.
obviously the fan at 100% gives the most airflow, but also creates the most noise and lowers the life of the fan some. a 4 pin connection and setting a fan curve is the better way to do it. this will adjust the speed of the fan based on temps. so you'll only get high speeds when needed.