There's (2) CPU fan headers, and you could use both of them for the H100 fans.
However, that's not how I did it.
Yes, on my personal X79 I do use three of the MOBO fan headers: 1. Rear exhaust, VRM AUX fan, and bottom fan in another case fan.
The Corsair 500R has (3) other fans: 240 side and 2x120 front, as it is they're connected to the case's 3-speed switched fan controller. I could use a splitter and extenders and run them all off the MOBO. Normally, I prefer a Fan Controller, and until I decide if I want to add a fully water cooled and blocked system I'm leaving it as-is.
In my instance, this is NOT meant to be a gaming system at all, and more a day to day. I run HUGE SQL tests at home and office where I code. SLI GTX 560's are okay, but nothing like my daughter's gaming system; the plan there is to replace the current 3-WAY with GTX 600's which is fully blocked / i7-980X system.