My firsthand experience may be of some help. I have a Gigabyte GA-EP45-UD3R -- an LGA-775 motherboard that is almost six years old. The machine has been through a few incarnations. It spends many hours "asleep," and so I only began to address thermal-control for noise reduction in recent weeks.
Go the Gigabyte's web-site download pages and look for the Easy Tune utility for the board. It contains a feature called Smart Fan, which should allow you to define a fan curve for a PWM fan powered off the CPU_FAN plug -- and possibly for other PWM ports on the motherboard.
If you can only control one fan (CPU fan) from the motherboard by temperature, you can spend $10 on a "splitter" like the Swiftech 8W-PWM-SPL-ST. The device plugs into the CPU_FAN header, but only for the PWM signal. You can then connect to the Swiftech as many as eight fans of mixed amperage and size, to control them with the CPU PWM signal and power them directly from your PSU.