OK, I bought a Corsair Obsidian 650D which comes with a manual 4 fan controller. I wonder if I should connect all my case fans to this controller or to the motherboard instead so that the fans can be controlled through software. Thanks.
I think it is more personal choice than anything else. I have 4 fans connected to my fan controller and two other ones controlled by motherboard. Just be sure to always connect your CPU cooler fan to the motherboard, anything else is up to you.
My motherboard has unused fan connectors while I have some fans connected directly to the PSU. Mostly a matter of convenience for me. That and the fact that I like my cables to be managed.
If you think you would screw up manually managing your fans then just ignore the manual controller.
There isn't a super huge benefit to letting the motherboard control the speed of a fan as compared to just letting the fan run at max all the time (directly connected to the PSU) unless you buy super loud fans.
I get the kind that are quiet even while running at max so I would rather just have max airflow and cooling all the time rather than letting my motherboard tell the fans they don't need to work so hard.
Any of them will work, it is mostly personal preference. I am not a big fan of the stand alone controllers, though, because people make mistakes and there is little to no benefit from human management if you have generally quiet fans.