I am currently building a computer with the cooler master 690 II advanced case. The fans on the case all come with 4 pin Peripheral adapters. Should I take them off and try to connect to the motherboard pins? There aren't even enough fan connections on the motherboard for all the fans I have. should I just use the 4 pin Peripheral connections provided? what if I want to regulate the fan speeds, the fan has to be connected to the motherboard right? Also, my asus board says that I have to connect the 4 pin cpu fan but my cooler master heatsink that I bought only has 3 pin connection, what should I do with that?
Connect the case fans using the black molex connections you can link them with other components it doesn't matter.
The HSF even if it's 3 pin will still connect to the mobo cpu fan header and that's where you want it.
There are 4 types of fan connectors, 2pin, 3-pin, 4-pin and Molex 4-pin.
Molex simply provides power only, so fan will run at full speed constantly. (unless its special fans that has a fan controller built-in)
Then there's the 2/3/4pin connectors for the Mobo fan headers, they are all compatible as long you plug then in the correct orientation (should be noted on the Mobo), the 2 pin is simply power, the 3-pin adds sensors for the fan speed, and 4-pins have PWM support.
Also, if it matters to you how loud the fans are, then connecting them through Molex will make them run at full speed all the time, which is noisy. If you have more fans than motherboard headers, I would recommend a fan controller. Zalman, Scythe, and others make units you can install into a 3.5" or 5.25" bay, and can power and control the speeds of multiple fans.