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JEMC said:

According to the manual (page 37), that JRGB1 connector is for up to 2 meter RGB led strips, not fans. That may be why TheLegendaryBigBoss had problems with it.

Fan headers can usually deliver up to 12V, and you can definitely use two or sometimes even three fans from one thanks to a fan spliter, but your mileage may vary. It's worth noting, tho, that you can't use RGB fans with those splitters as they use more power, obviously.

To solve both of your problems, you could try to find a fan controller hub that has enough room for all your fans. Some of them are manual, meaning that you need to open the case to change the light or the fan speed, but others connect to a spare USB header and allow you to control the fans from Windows. Many brands have their own HUBs, but some of them are locked to their own fans, creating a closed echosystem.

So I currently am using a fan controller hub (which lets me control the fans and rpb with a remote controller), and wanted to move away from that. At least from the one I am using.

Because the fans I have that came with it cannot plug in to the motherboard, as they have different connectors than usual. And I'm about to get a new CPU cooler, which has a normal connector.

That and because the hub seems to be malfunctioning. Whenever I boot up my PC for the first time in a day, the case fans will get extremely loud, until I shut off my PC. Wait 10 seconds or so, and boot it up again. Then they function normally.

Not sure if there's a way to fix that. Someone suggested I reset the CMOS battery, but I want to look up exactly what happens if I do that.