I am not sure how fans work. For example, on the ASUS M5A97 LE R2.0, are there places I can plug my fans into? When they are plugged in can I control them from the BIOS? Do I even need to plug them in or can I just use molex?
You use the small 3 pin or 4 pin connectors or use a 4 pin molex to 3 pin or 4 pin adapter for fan power. you use one or the other but not both. Yes the Asus mother board may be able to control the fan speeds in bios.
If you want to get creative with it you could use some Bit Fenix cables
one example would be this http://us.ncix.com/products/?sku=71198&vpn=BFA-MSC-M33F...
it is the 12V version and would spin your 3 pin fan at full blast all the time, or you could get the 7volt or 5 volt version and always have slower and quieter fans.
Or you could just get quiet fans to begin with from Noctua or Corsair.
Hope this helps.
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.