I don't know if I'm doing something wrong here, but each of my fans are 4-pin connectors. I have eight fans in total, with the two attached to my radiator using CPU1 fan slot (shared connector), and the top mounted fan at the front using the CPU2 slot. Out of the eight fans and seven slots, I only receive information in SpeedFan about three fan slots and they are the default fan slots that have the "Smart fan" setup in the BIOS. As my radiator fans are using a shared connector, they can't be controlled by SpeedFan, but can be controlled by CorsairLink anyway.
 
The problem I have though is that there are five other fans, all with 4-pin connectors, unable to be configured manually by any software... If you can't control these fans manually, why is there an option to change them between DC and PWM? I thought a 4-pin connector was to allow management of the fan?

All fans are plugged directly into the motherboard via their 4-pin connectors. The only two that aren't are the radiator fans which are plugged into the Corsair 115i pump fan controller headers.

Ok but why? Is there no way to get control of the fans?

The only thing you can do is have them follow the step profile of a controllable header, should be three of those.