Even though you have a camera that manages higher ISO well for you, I would still suggest using the lowest possible ISO you can until you get raw base files that suit you and hold up to the processing you want. That way you can eliminate the higher ISO as a potential trigger for the "noise" that is bothering you. I would also use the old fashioned approach of ETTR - expose to the right as far as possible without blowing any highlights - while you experiment with capture. If the "noise" is still present with the lowest possible ISO, then ISO may not be a factor. The best cloud photographer I know uses this approach with a wide array of camera bodies. And yes, you are wise to explore what your camera's brain decides about ISO adjustment when it's set to auto. I'm sure there are controls that will let you limit its choices. My personal preference with clouds, or other massive amounts of water vapor such as fog or big powerful waterfalls is to shoot with full manual control including ISO. All water vapor is comprised of droplets which may look like noise in the capture but may not really be noise of the kind we are used to, and don't respond well to noise removal software. To get a look you want, you may have to rely on software solutions that let you add some blur in a masked layer or negative clarity with a brush to smooth things out where you want it smooth.
If I'm using noise reduction I use it before other raw adjustments. When adding clarity/contrast, new versions of ACR (/Lightroom) offer a lot of help for isolating various areas and treating them individually so that adjustments are not applied universally. That becomes important with different areas of brights/darks like your clouds. There's also various tools in PS, but I'm not sure they are all there in Elements.
Someone mentioned Silver Efex. It is my favorite too for black and white conversions of highly structured clouds like in your captures.
This is a fascinating project, capturing the art that lives in the sky.