Your cap will help keep it out of the water column in normal day to day use. If you have a high clay volume in your substrate, take care when uprooting/moving plants, it'll make a terrible mess. Some folks have recommended clipping plants and leaving the roots, which work for stem plants, but not for things like crypts or lotuses.
Water changes and filter floss will help clean the water out when it does get cloudy. It'll settle out eventually. The more cap, the less mess. Good luck! Plants will love the iron from the clay.