Case fans are mainly sold with a 3pin sometimes 4pin(PWM). The headers on your motherboard are there for you to plug fans into, they should accept either 3pin or 4pin connectors. and Yes, if the fans are plugged into the motherboard via the fan headers scattered around, they can be controlled by the bios. I believe there is software you can get to then control them from within windows. If you do choose to power them via molex, they will be running at full voltage, and can not be speed adjusted.