The 6 pin connectors at the Thermaltake controller are GND, DI,DO,5v, nothing, 12v from top to bottom. Now, I am assuming that DI is "digital in" and DO is "digital out". If so, then you SHOULD be able to use 12v and DI lines if the DI line is the "tach" signal to control your fans. You have to look up the pin out for the ATX fan connectors to try this. I don't think you would need GND connector as it appears to ground both the LEDs and the fan, so as long as you leave that as is the fan should have GND. I've been meaning to try this for sometime, but have not gotten around to it. You can buy the 6 pin connectors that fit the Thermaltake controller from Amazon ("10 Sets JST PH 2.0MM 6 Pin Female Single Connector with Flat Wires 100MM 1007 26AWG") and then you would need some 4 pin ATX fan connectors which you can buy other places (ebay).
Now, I'm making SEVERAL assumptions here. First, DO is the LED signal line, that is what controls the LEDs. Second, DI is the "tach" signal from the fan. Either or both of these could be wrong. Like I said, I've been meaning to try this, but it's WAY down on my list. Hope this guessing may help someone. I figure you can send the 12V and DI wires to a fan connector and plug that into your MB fan controller making sure you are connected to the correct pins. This SHOULD make the fan visible to the MB, but again, a bunch of assumptions.
If I EVER get around to actually trying this, I'll post back, but don't hold your breath. My MB does not support ARGB, so I'm in even worse shape. I can't even try Asus AURA unless I buy the Asus ROG terminal, so all I'll get from this is (maybe) fan speed control.