I use Corsair ML120s on both of my 1080 Ti Hybrid kits.  I got myself a fan hub from Silverstone and plug all related fans (4 in my case since I do push/pull on both radiators) into the hub, then plug the hub into a motherboard header and control the fans using the BiOS.  That's basically what you're planning on doing, so yeah, plug the fan into the motherboard as you said and use Speedfan to control it.

Wait, your radiator is on the floor portion of your case? As in below the GPU, or rather, the pump?

Uh, yes it is affected. There's air in there that you're constantly shoving through the pump by having the rad flat with the tubes coming out the top. Yes, my wording earlier was wrong to some degree as my reasoning directly relates to the rad itself.
 
The pump relies on having no air go through it once its in (stable) operation.
 
The impellers lose efficiency when there's an air bubble in the pump area because air is highly compressible whereas liquids are (largely) incompressible. And that's assuming air actually gets pushed out of the pump before being sucked back in later.
 
If the air never leaves, then heat is building up in the air pocket.
 
And finally, the impeller moving in and out of an air pocket generates noise/vibration.
 
Try moving it to the rear as exhaust. At the very least, have it vertical with the tubes coming in at the bottom. As the reservoir itself can hold any and all air at the opposite (top) end.
 
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On a separate note, I'm not sure having an exhaust on the bottom is all that great of an idea either.
 
I believe having fans blow down onto a surface that close can create back pressure and that might amplify "resonance." Though it's probably realistically minor and overall insignificant.
 
But my actual concern is if enough of it flows to the front, it just gets sucked right back into the case through the intake.
 
I have a couple of general rules I follow when it comes to managing airflow in a case.
 
One: Most important of all... avoid sucking in exhausted air as much as possible.
 
I do that simply by having my intakes in front and below, while the exhaust goes out the rear and top.
 
Two: keep airflow (volume) for intake and exhaust as similarly as possible.
 
That is either done by physically having same number of similar speed fans as intake vs exhaust. If not possible, then have adjustable speed fans match the overall volume. This is to avoid having back pressure when the intake is too high (air moves slower in the case than the intakes can ideally push) or dust accumulation when the exhaust is too high (air will be forcibly sucked in from any and all openings around the case... usually unfiltered).
 
Opinions aside about the case, many cases are set up with not too different ideas regarding airflow... and the proof is usually in where the filters are. Intakes are filtered while exhaust are not. For you case, that's front and bottom.
 
Many PSUs have fan layouts such that it pulls from below and pushes out the back. For your case, the PSU will act as an exhaust. So, if you move the hybrid to the rear as exhaust, you have two exhausts. Then leave the front and add one or more to the bottom as intakes. The more intakes you have, the lower the speeds they can be to match the two exhaust. Since CPU AIO will need some minimum level, the bottoms ones will be even slower.

All of the AIO coolers have air in them. All. They are all made by the same company who owns the patent after all. The radiator should be somewhere above the GPU and the hoses should be at the bottom of the radiator. Even EVGA representatives recommend this solution over and over again. The top of the radiator should be the highest point in the AIO system so that the air can collect there. If you do it that way, the bubble cavitation sound will go away within a period of hours. If you don't do it that way, the bubble cavitation sound will never go away no matter how many times you replace it.

With the earlier hybrid kits and to some extent, the current ones... the reason is because the kit mounts onto reference designed PCB.
 
That design is only for one fan.
 
So the options are,
 
1) speed control both fans & pump together. vary speed on the pump isn't bad, but letting it stop surely is.
2) speed control both fans and bypass the pump. requires rewiring in the pump.
3) bypass the stock fan and pump to control only the rad fan. also requires rewiring in the pump.
or the current, 4) control stock fan as it's already wired for it and save some $change by using just two wires for power/ground for both pump and fan.
 
Especially when the pump is designed by a completely different company in the first place.
 
With custom PCB, then they can have multiple fan/pump headers and do whatever to each separately.
 
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As for controlling the fan... another option is to replace it with something else that plugs into the motherboard and have whatever software there control it. Though it might a little tricky to set up a fan profile through the motherboard to be based on GPU temps.