Just leave the AC97 disconnected. Plug in the HD audio connector to the F_Audio header on the motherboard. (page 26 in your MB manual) Modern cases provide both connections in case you are using an old MB.
Besides the CPU FAN header, that motherboard has 3 x aux fan headers; SYS_FAN1/SYS_FAN2/PWR_FAN. You can dispose of the Molex adapters on the fans and plug the small connectors into those headers. That is the normal way to do it. (page 23 of your MB manual). Or, if you prefer, you can leave the large Molex adapters connected to the fans and plug them directly into Molex connectors from the PSU. Your choice.
Unless you have an old PC, you will use the HD Audio instead. AC97 is a legacy connection for old motherboards.
But it would help if you told us what PC/case and what MB you are using.
Also, as a side question, the HAF 912 has fans with both female and male Molex cords. I have already plugged the females into the males of my PSU, but what do I do with the male fan cords?
Just leave the AC97 disconnected. Plug in the HD audio connector to the F_Audio header on the motherboard. (page 26 in your MB manual) Modern cases provide both connections in case you are using an old MB.
Besides the CPU FAN header, that motherboard has 3 x aux fan headers; SYS_FAN1/SYS_FAN2/PWR_FAN. You can dispose of the Molex adapters on the fans and plug the small connectors into those headers. That is the normal way to do it. (page 23 of your MB manual). Or, if you prefer, you can leave the large Molex adapters connected to the fans and plug them directly into Molex connectors from the PSU. Your choice.