The bigger question is, will your fan controller do anything ? The Antec 1200 case fans are designed to work with the provided switches and variable speed knobs. Two wires go to the Molex meaning that there will be no rpm indication back at the controller.
I chose to sleeve all the fan wires so I removed all the Molex connectors and changed them to 3 pins. Fairly easy task with the proper tools and components from FrozenCPU.com However, either way, you will still not have fan speed control whether you use the MoBo headers or a fan controller. Right now I have the two "optional" Antec 1200 case fans (the ones you buy separately and that come with 3 pin connectors). Although these also have the 3 speed switch, they do work with my fan controller (Asus OC Station). The rear case fans do not, and the bigboy top fan does not. I saw no reason to connect the front case fans as the variable speed knobs are just fine for fan control as they are easily accessible.
Antec, in providing speed control with the case, effectively precludes the option of using fan controllers with the black case fans. Again, for whatever reason, their clear plastic fans work just fine.
http://www.newegg.com/Product/Prod [...] 6835209011
As for whether you can power them as you suggest will depend on your fan controller's abilities. If it's soemthing like the NZXT LX, I'd say be careful. If it's the NZXT Sentry 2, it should no problem. To make this determination, if you check the Antec site, you'll see:
http://www.antec.com/pdf/flyers/BIgBoy_sellsheet.pdf
Big Boy 200mm 0.30 amps
http://www.antec.com/pdf/Fan_Comparison_table.pdf
120mm 0.24 amps
So if you want to combine the 3 front fans at 0.72 amps and your fan controller can handle 0.50 amps, you gonna toast it.
I also wouldn't mix non identical fans.....combining the two rear 120mm for example should be fine. That's what I did but I useda sleeved version of this:
http://www.frozencpu.com/products/ [...] itter.html
Again, I can do that as my fans no longer have Molex ends, the cables are sleeved with 3 pin connectors.
You can also use these:
http://www.frozencpu.com/products/ [...] g2c251s634