Covering with stones is not needed, as long as there are no large items of bark, styrofoam, perlite, charcoal, and so forth, in your soil, but you should have those things in the soil, in order for the plant to do well and cope with amount of water it will be subjected to. Organic soil is a misleading term, as perlite and charcoal are still organic, but if eaten, while not toxic, can block the intestines.
As far as your water marks, they are harmless, very hard to to remove and just unsightly. Get a couple gallons of distilled water, mix 2-4 TBS of Murphys Oil Soap concentrate in them, warm them to bath water temperature, and spray the plants throughly, then rinse, rinse, rinse with water that contains no minerals, such as distilled or reverse Osmosis. Rinse until you don't see or smell the soap. You won't remove all of the stains this way, but you will remove most residues, dust, spider mites, and other contaminates. You can add a squirt or 2 of dawn dish soap ( you don't want an aggressive soap that will destroy the natural waxy coating on the foliage ) and a 1/4 cup of white vinegar in the mix, for extra umph, but rinse this quickly, as vinegar can cause brown marks on the leaves. Club soda works in place of vinegar and may or may now be easier on the foliage, or carbonated water....it's the acid that will dissolve the basic mineral deposits.