I'm going with the fan controller first and later I'll try MB fan control and see which I like best. I initially favored MB control.
What is your cooling strategy -- Water, or heatpipe cooler?
My view -- thermal control of certain fans -- not essential -- but desirable. I always power my CPU fan and exhaust fan(s) from motherboard headers. ASUS boards are very good with BIOS-with-thermal-control of fan headers.
That being said, I looked at the NZXT specs. They've included a digital fan controller with 15W per channel. Does this controller provide for THERMAL control of fans connected to it? If so, it also would include two-pin thermal sensors with stick-on thermal tape. If not, then I'd guess it's a "set-it-and-forget-it" arrangement.
15W per channel would allow for 12V fans up to -- even slightly more -- than 1 amp. Especially if this NZXT controller DOES NOT provide for thermal fan-speed-variation, I'd control your CPU fan and/or exhaust fans from the motherboard -- at minimum. Use the NZXT controller for additional input and exhaust fans.
ALSO -- your case has some features similar to my CM HAF -- large, low-rpm fans. My HAF has three mounting locations for these latter. I only use two of them -- front and side-panel. I block off the top-panel fan vent with black foam art board. Unless you have something that gets very warm at the case top, or you don't have adequate exhaust, the other two input fans should be more than enough to provide the throughput you want.