Also, I have a 4 pin splitter I could plug into the motherboard fan header, but only one of them is 4 pin on the fan side. Why?
In reference to the splitter.
Assuming you mean like that above. Two fans into one splitter. One of the female ends has 4 pins but the other has 3 pins. 2 fans sending information back to the same motherboard header causes issues. The splitter uses the RPM signal of the 4 pin fan and assumes they're both the same speed. You'll get one speed signal from the header on the motherboard, but both fans will be at the same speed provided they're the same fans.
As for why they won't work with the CLC, the manual is awfully bare and gives no real hints. Seems like people have complaints with the software as well.