The best way i've found to paint ballast is to lay the rail, then paint your tile in it's base color - I use Dry Grass - and then paint the ballast liberally on each side of the tracks. Turn the brush down to a Radius of 15, and a strength of .15. Hit just the jagged points of the ballast, clicking on the mouse lightly, as if you were tagging a boxcar with a can of spray paint. Keep doing this until the jagged edge is fairly blended into a straight line. If you do to much and make a hole in the ballast, switch over to Gravel and repeat the steps.