As I have never owned this cooler I can only go upon the reviews I've read and my experience with the Coolit Eco and Corsair H60 sealed unit water coolers that I've owned. (Am currently running the Corsair).
Basically, if I read the imfo. correctly, the Antec comes with 2 x 4 pin PWM fans , which plug into the pump housing with , then two cables running from the pump housing ; the 1st being to provide power (partic. for the pump) which looks to be a 3 pin connector and the second is a usb(?) connector to plug into a motherboard usb header.
All having been connected and the software installed you can control the fans (and pump?) via windows . Again if I read correctly , the software provides 2 built in modes ,Extreme or Silent and the third 'custom' which is , of course, much more hands on. - If you are using this software then I believe that it is extremely unlikely/impossible that you can control the fans through the motherboard Bios!
Both the Cool-it and the corsair work in a different way i.e.:-
1. The power to the pump is seperate from the fan(s). - a 3 pin header only. (Designed I believe to be on at all times)
2. The fan(s) being powered either by a 3 pin fan header (not, I think, PWM control) or via the cpu fan 4 pin header (which often/usually will allow for PWM control via he bios/board ; assuming that the fans are 4 pin).
Currently my radiator fan ( it used to be fans but I found that it did not cool that much better , if at all, than a single fan ) is a 4 pin plugged into the cpu fan header and with speeds controlled via PWM/ settings in the bios. (when running 2 fans I had to buy a splitter to fit them on the cpu fan header).
Overall I would have hoped that the Antec software would have more options than the Bios and as it's through windows it should be a lot easier to adjust on the fly - BUT if you plug the fan(s) into the cpu fan header on the motherboard they should work. (although it is possibly the case that the Antec DEMANDS that they be plugged into the pump housing connector for it to work at all- be careful!).
Hope the above is of use - Sorry if I've been a bit long winded
