I cant see itll take that long to clear, but with how muddy your water is, Id probably clean out the filter sponges, wool, or anything else you have in there to trap small particles daily. Thatll keep things running at full speed while it clears the muck away.

I dont think theres any way of adding water to a new substrate without kicking up at least some sediment.. I woudlnt worry about it, itll sort out.