Good start there James.
Question 1: I use an ink eraser to clean the tracks. Those dark grey ones, not the soft pink ones.
Question 2: thoses "stones" are called Ballast. At our club, we sprinkle the ballast between the ties, use a soft brush to spread it so the tops of the ties are seen and the flangeways are clear. Then we use "wet water/glue" to glue it down. "Wet water/glue" is 50% white glue, 50% water then a drop or two of dish detergent (to break the water tension). The "wet water/glue" is mixed in a used glue bottle and just dribbled between the tracks.
After the glue has dried, usually overnight (or next meeting at the club), carefully use the small brush again to remove any loose ballast. You don't want loose ballast getting in your locomotive gears.
Hope this helps.