Actually, your mobo has almost all you need for what you want. But I think you are over-thinking what you want! Furthermore, doing this easily REQUIRES that ALL of your fans be of the PWM type (4-pin fans), and you'll need some very simple additional items.
FIRST, you need to understand fan controls. Everybody talks about fan SPEED control, because that is what we all see changing. But that is NOT really what is important, and that is not what a mobo automatic fan control system does. The real focus it TEMPERATURE of important components. A mobo actually runs TEMPERATURE control systems that manipulate fan speed as a tool, NOT as the final aim. Your mobo has at least two such systems, and can have more depending on how you configure them - your particular mobo has more abilities here than most.
EACH fan control loop operates this way. At the time of initial set-up it recognizes the particular hardware installed and sets a number of parameters for the loop appropriately. When running, it constantly uses the signal from a TEMPERATURE sensor to measure the temp of a key component it is focused on, compares that to the proper target temp for that, and uses the difference to set the speed of the fan that cools that component. If the temp rises it speeds up the fan; if the temp is unchanged, it leaves it as set; if the temp falls it slows down the fan. There is a max speed the fan can run, and if the temp cannot be kept below the component's max limit at full fan speed, the system will send out an alarm and take action to reduce performance and heat build-up. On the other end if the temp goes really low the fan will be reduced to minimum speed, but NOT turned off. There is no harm in running a fan slowly. Most importantly, if the fan's speed control is set too low it will stall and then there is NO cooling, and the fan will not re-start until its signal is increased by quite a bit. So it's better NOT to let the fan stall.
Normally there are two temperature control systems on a mobo. One is for the CPU, and the temp sensor for this is inside the CPU chip, built in by the CPU maker and fed out on one pin. This sensor guides the fan connected to the CPU_FAN connector, and in your case the CPU_OPT connector.
The second system is for case ventilation, and it is guided usually by a different sensor built into the mobo by its maker. It guides fans connected to the SYS_FAN ports.
Your mobo has more than these. It has four SYS_FAN ports and it appears (see your manual, pages 3-36 to 3-38) that EACH of these can be configured separately. Moreover, it has more than these two common temperature sensors. It has another in the PCH controller hardware, and an optional thermistor sensor on a cable that plugs into a mobo socket labeled T_SENSOR. It appears that for EACH of the four SYS_FAN ports you can select which temp sensor that control loop will use AND you can customize the relationships of temperature to fan speed IF you set that loop to the MANUAL temperature control profile. This gives you a lot of power to customize, BUT it means you will have to learn a lot, too. For each loop you customize (rather than leaving it in default Standard mode) you would have to know what temperature you are controlling, what its target should be, what its max and min temps should be, and some idea of how the fan speeds should be adjusted to get that to work.
OK, so it appears that you can set up custom cooling controls for the CPU AND for four other case ventilation systems. Now, how do you arrange for multiple fans on some or all of those separate control loops? The key is that you MUST be using 4-pin (PWM type) fans AND you MUST have each of your SYS_FAN ports set to PWM Mode, not to DC Mode. Then you'll need some simple PWM splitters and/or adapters. Your post suggests there are three different ways you want to connect things, so I'll address each. The guiding limit it that any mobo SYS_FAN port normally has only one connector but can support up to TWO fans using a splitter. It you want more than two fans on one port it cannot supply that much power and a different arrangement is needed - that's where we get to the adapter.
OK, so for the cases where only one fan is connected to a SYS_FAN port, there is no confusion or option - it's straightforward.
For using TWO fans on one SYS_FAN port you need a 4-pin Y-splitter like this:
http://www.newegg.com/Product/Product.aspx?Item=N82E16812162026&cm_re=pwm_fan_splitter-_-12-162-026-_-Product
It sends power from that SYS_FAN port to both fans, along with the PWM control signal. Now, every fan generates its own speed signal as series of pulses it sends back to the mobo port on Pin #3, but only ONE fan can do this. So a good splitter simply does NOT send back the speed signal from one of its two fans, and that fan will never have its speed measured.
For the case of MORE than two fans on one SYS_FAN port, you need a 4-pin PWM adapter that is a little different. This is just a group of cables and looks like this.
http://www.newegg.com/Product/Product.aspx?Item=N82E16812423166&cm_re=pwm_fan_splitter-_-12-423-166-_-Product
It has one connector that goes directly to a Molex 4-pin output connector from the PSU to get all the power needed for all the adapter's fans. It has one female 4-pin connector that plugs into the mobo SYS_FAN port. Then it has several (3 to 5, typically) male 4-pin fan output connectors. It supplies power to each fan from the PSU, not the mobo port. It supplies the PWM control signal from the mobo port to all of its fans. And it sends the speed pulse signal from ONE of its fans back to the mobo for measurement.
I emphasized the need for 4-pin fans for all this. The reason is simple. Of you plug a 3-pin fan into a 4-pin port operating on its normal PWM Mode, the fan will always run at full speed. A PWM Mode port cannot control the speed of a 3-pin fan.
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