Most of the time a side-panel blow-hole duct would suck air in and onto the CPU cooler. I've cut blowhole ducts in most of my systems, but I've been re-thinking this lately. Let me get back to that thought in a minute.
Just for the matter of noise, it would be better if you can duct the side-panel blow-hole to the top of the CPU so that the CPU fan can only draw air from the blow-hole. Then you can dispense with the side-panel fan, which is bound to be noisier, just for its proximity to the case-panel.
Also, you say you have a rear intake fan. Usually, intake fans are deployed in the case-front, and exhaust in the case rear. This is not some rule-of-thumb, but you should balance the air inflow and air outflow in the case by getting your fan CFM specs, making whatever linear extrapolations are necessary for the speed you intend to run each fan. Filtered intake fans will not meet their full CFM spec even at top speed, but you should be able to match intake and outflow approximately.
Now back to the other issue. I now use a foam-art-board motherboard duct, which forces air over the motherboard before it is exhausted. Part of the logic of using such a duct involves having case intake fans with high throughput. The duct separates new "cold" air from "warm", and the pressure outside the duct should be at least as great as what it is inside. I've been able to eliminate much noise by closing off my blowhole and tuning up my front-panel intake fans just a tad. The net change in noise seems to be on the loss side, and that's good.
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