The brown tinge is diatoms. All tanks go through a diatom stage. Once they absorb some of the silicates in the water column and substrate, they normally start to disappear.
As far as cleaning filter materials, it sounds like you're doing a fishless cycle (GOOD) and you shouldn't need to clean or change any of it unless there's a clog during the cycle.
What kind of filtration do you have?
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