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If you didn't rinse the sand really well then your tank will cloud up whenever the sand is disturbed. With my pool filter sand I washed it really well and I can stir it up without the water clouding. Just takes a lot of time to do correctly.
Bubble_B0y has a good idea with the plate trick. Works very well. If your tank is too small for a plate than use a cup, just go a bit slower.
Yes i used a plate when i filled the tank, but it got pretty dirty once I added the "goo" from the old substrate. I did a pwc and that's when the water seemed to get cloudy. There are no fish in the tank so if I need to I can redo the sand - would that disturb the cycle?