If you run the sump now most of the cloudiness will settle in the sump, and then you can suck it out of the sump. I often will use a turkey baster to stir up the detritus in the show tank and allow it to settle in my sump and then do the water change from my sump. It also helps when first establishing your tank to use a siphon to clean the top layer of sand as that is where most of the detritus (or in this case the really small particles of sand) will settle. As far as your question as to whether it will cloud any time you stir the sand the answer is no. What you are seeing is very small particles. Before I put my sand in, I rinsed it in a 5 gal bucket for about a half hour to get rid of this stuff. But it is too late now, if it makes you feel any better my first tank was rushed and took me several days to clear. HOB filters aren't a bad Idea. I hoped this helped.