If you're fans are connected directly to the pump and THEN onto the motherboard then the only way for you to control them is through corsairs own "Corsair Link 2" software. And I hate to be the bringer of bad news but it doesn't play well with others. AIDA64, Fan XPert2, or any other monitoring software will conflict with one another. You could always plug the fan directly onto a motherboard fan header and control it via UEFI or Fan XPert. Corsair Link is also in beta for Windows 8.1 at the moment so you should be aware of that.
Every program will report different temps and rpms, ASUS"s AISuite only reports every second while others will report on the fly. AIDA64 and real temp are both well made programs and should be reading accurately.
You could absolutely get a good fan controller to handle the fans if the noise/software is bothering you. You could also grab some silent fans for the stock ones on the pump are notorious for being noisy. At the end of the day its you're build and you're preferences, experiment with settings and you will find the best configuration to suit you're needs.
Corsair 750D | Maximus VI Formula | 4770K @4.5 | H100i P/P | Vengeance Pro 16GB 2133
ASUS GTX 780 DCII | Intel 520 SSD 120GB x2 | EVGA Platinum 1000W | Windows 8.1