Will an 8-way SATA powered PWM fan splitter work with my motherboard's fan controller software?

Sorry, no, that won;t work.

The problem here is that the Swiftech hub and the Coboc unit (which also is a hub) both do the same thing. They draw power for all their fans from the PSU so they don't overload the mobo fan header, and they pick up a PWM signal from one mobo header to share with all their fans. This means that ONLY 4-pin fans can be CONTROLLED using this system. NO 4-pin supply operating in PWM Mode can control any 3-pin fan, and that is what you say you want to use.

For some cases there may be a way to do what you want. Post back here with this info:
(a) how many fans of each type - that is, 3-pin and 4-pin - for case ventilation only? Don't include the CPU cooling system.
(b) exactly what mobo - make, model, and version number if there is one - do you have? That allows us to see its details in its manual.
With that info we can advise ways to connect and use mobo-based control of fans.

So for case ventilation fans only, you have four 3-pin fans. It is possible you might try adding others later by connecting them to the PSU via adapters.

Using your four 3-pin fans under mobo automatic control will be easy. I say that because two factors are satisfied in your case. First is the general rule: you can connect up to two "normal" fans to each mobo SYS_FAN header, but not more. Second is that any 3-pin fan can ONLY be controlled by a mobo header operating in Voltage Control Mode.

To take the second rule first, I see in your mobo manual on p. 12 that both SYS_FAN headers have labels showing Voltage Control on Pin #2, and NC on Pin #4. So both ARE what you need to control 3-pin fans, even though they are installed with four pins. The 4th pin on each is just non-functional decoration.

To connect two 3-pin fans to one mobo SYS_FAN header you need a simple 3-pin Y-splitter. In your case, of course, you will need two to handle four fans on two headers. You need a couple of this type:

http://www.newegg.com/Product/Product.aspx?Item=N82E16812423168&cm_re=3-pin_fan_splitter-_-12-423-168-_-Product

A 12" long version exists also if you need one.
This unit passes the speed signal from only ONE of its two fans back to the mobo for display; the other is ignored. This is the correct way to design these splitters.

My guess is that all four of your fans are common 3-pin type with female connectors about 3/8" wide with three small holes. A "2-pin fan" usually is one designed for connection directly to a PSU output, and hence has only 2 wires from motor to connector, and the connector is a much larger "4-pin Molex" male with only two of its four pins inside the shroud. If you really do have two of those "2-pin fans", connecting them to a standard 3-pin male fan output is a bit tricky. The problem is that I have never found an adapter to connect a male 4-pin Molex to a male fan output. The only route I have found is to cut off the large Molex connector and either replace it with a standard 3-pin fan female connector, or solder its wires to the wires of another fan so they operate in parallel electrically. If you have to do that, post back here for hints on how to match wire polarity.

So for case ventilation fans only, you have four 3-pin fans. It is possible you might try adding others later by connecting them to the PSU via adapters.

Using your four 3-pin fans under mobo automatic control will be easy. I say that because two factors are satisfied in your case. First is the general rule: you can connect up to two "normal" fans to each mobo SYS_FAN header, but not more. Second is that any 3-pin fan can ONLY be controlled by a mobo header operating in Voltage Control Mode.

To take the second rule first, I see in your mobo manual on p. 12 that both SYS_FAN headers have labels showing Voltage Control on Pin #2, and NC on Pin #4. So both ARE what you need to control 3-pin fans, even though they are installed with four pins. The 4th pin on each is just non-functional decoration.

To connect two 3-pin fans to one mobo SYS_FAN header you need a simple 3-pin Y-splitter. In your case, of course, you will need two to handle four fans on two headers. You need a couple of this type:

http://www.newegg.com/Product/Product.aspx?Item=N82E16812423168&cm_re=3-pin_fan_splitter-_-12-423-168-_-Product

A 12" long version exists also if you need one.
This unit passes the speed signal from only ONE of its two fans back to the mobo for display; the other is ignored. This is the correct way to design these splitters.

My guess is that all four of your fans are common 3-pin type with female connectors about 3/8" wide with three small holes. A "2-pin fan" usually is one designed for connection directly to a PSU output, and hence has only 2 wires from motor to connector, and the connector is a much larger "4-pin Molex" male with only two of its four pins inside the shroud. If you really do have two of those "2-pin fans", connecting them to a standard 3-pin male fan output is a bit tricky. The problem is that I have never found an adapter to connect a male 4-pin Molex to a male fan output. The only route I have found is to cut off the large Molex connector and either replace it with a standard 3-pin fan female connector, or solder its wires to the wires of another fan so they operate in parallel electrically. If you have to do that, post back here for hints on how to match wire polarity.

Yes, that actually would work. A Y-splitter merely connects one wire from the mobo port to pins of both its output connectors (excepting that for Pin #3, the speed signal line). Using a 4-pin splitter merely means that the 4th hole of the female connector at the mobo header connects to an unused pin on your mobo, and the 4th pin of each output connector is NOT connected to anything on the 3-pin fan's female connector.

The mechanical and electrical design of male and female connectors for computer fans ensures they can be used together in logical ways. Each female connector has a groove on its side aligned outside Pins 1 and 3. Each male header on the mobo has a plastic tongue sticking up beside those 3 pins. The connectors can only be put together one way. On 4-pin connectors, the groove and tongue still are aligned with Pins 1-3. the result is that any female connector can fit any male header. Electrically speaking the use of the pins is very similar. If you mis-match by plugging a 4-pin fan into a 3-pin port, it WILL work and WILL be under speed control by the header that uses Voltage Control Mode. If you mis-match the other way (3-pin fan into 4-pin header using PWM Mode), the fan will work, but with no control - it can only run full speed all the time. But the main point of all this, OP, is that your 3-pin fan's female connectors WILL plug into the 4-pin splitters' output male connectors and they WILL work in your situation because your mobo headers actually are not true 4-pin PWM headers - they operate in voltage Control Mode..