no need to have lights on if tank is cycling. you're just exposing the rocks and sand to algae growth.
those spots are likely diatoms and should go away on their own, but if it bothers you - you can sift it out or increase water flow in the tank (adding or repositioning a wave pump or gyre), or increasing the return flow of your return pump and getting a RFG(random flow generator) from @Vivid Creative Aquatics to help