I recently switched cases and now have 3 fans. In this upgrade, i also purchased a MSI z77a-G41, and am no longer sure how to control the case fans. I have tried speedfan, but unfortunately, the software has only let me monitor the gpu fan speed.
Go into the bios. Under advanced mode, there should be a Monitor (or something of that sort) option. You can choose Auto or the % you want each fan to run at.
Damn, Must just be using really poor fans. I have all fans set to 50%, but yet its still makming a fair bit of noise. Oh well, might have to look at different solutions for noise control.
There is also MSi control center. Download that. I have a Z77A-g43 mobo, and use that to post RAM clocks, can also control fans through the program. Only two though I think it varies from each model of mobo.
Edit: it will be under smart fan control, pretty much the same as the BIOS options. It does allow me to set a custom profile though. I've used it a couple of times playing with benchmarks.