Thanks for the Best Solution.
If you're using the Corsair's speed controller then you CAN control the case fan speeds as you see fit, and that is better than using the mobo's ports with no control.
However, I do suggest you use the mobo's port for the CPU_FAN and let it control that fan if possible. The CPU fan is handled a bit differently. Besides controlling its speed, the mobo usually does one other thing. On many mobos it also monitors closely the actual fan speed. You see, the fan motor itself generates a fan speed signal (two pulse per revolution) that is sent back to the mobo on the third wire (Yellow) of the 3-pin fan connection. (On a 4-pin fan, the same signal is generated and sent on this line, but the wire color code is different.) On many mobos today that signal for the CPU_FAN is checked constantly; if it stops, the mobo assumes the fan has failed. Without even waiting for the CPU's internal sensor to signal a high CPU chip internal temperature, it can send out a warning beep signal and shut down the entire system quickly to avoid possible overheating and CPU damage. This is just an extra protection mechanism for the CPU. IF you decide not to power your fan this way (and do it via the case's controller) the fan's speed signal can't get to the mobo and this system cannot operate. IF your mobo has this protection feature and you connect the CPU fan to the Corsair's controller, check in BIOS Setup where the CPU fan is controlled. It may have a setting to IGNORE the CPU_FAN speed signal, and you should set it this way so that it does not believe (falsely) that the fan has failed because it has no signal.
On some mobos, that feature I mentioned of allowing you to set the fan port to either 3-pin or 4-pin control mode it available only on the CPU_FAN port. So again, check your mobo manual or the BIOS Setup screens to see whether your mobo has this feature to make it easier to use your 3-pin fan on this port.
A minor point when you control fans from the Corsair's controller. The mobo has a way to monitor and display the speeds of each fan connected to its ports, although only the CPU_FAN speed is given intensive checking as above. When you connect instead to the Corsair's controller the mobo cannot do this. So, unless the case's controller also has a speed measuring and display feature in it, you will not be able to see your fans' speeds. No big deal in most cases, except that you won't have any continuous verification that all your fans are working OK.