Sometimes thinking outside the box is good. Years ago I was at the arts and crafts store Michaels and found containers of coarse stone granules. These are typically used for making clear-glass fake (or real) flower containers, where layers of colored sand are used in the container for decorative touches. These are available in a several colors, two of which I show here, namely gray and black. Size-wise they have granules that measure between 1 and 3 inches in S-scale. Perfect for yards, coal industries, or hopper car loads. One of these containers costs about $4. I believe "Ashland" is a brand name owned by Michaels.
(external link: Ashland by Michaels)
For hand-laid track, I apply the ballast before installing the rail. It is so much easier that way. I start the process of ballasting by using a small artist's brush and cover an area with full-strength white glue. I then sprinkle a thin layer of the ballast on top of that glue. I keep going like that, one section at a time, until the whole area is covered. I let that dry at least overnight. Next, I apply a second thin layer of the ballast, making sure to keep it below the tops of the ties. To adhere this second layer, I spray isopropyl alcohol over a section, followed by a spray of 50/50 diluted-with-water white glue. I usually put a drop or two of dishwashing soap in the glue mixture. The alcohol and the dishwashing soap help break up the surface tension of the glue/water mixture, so that it will flow freely and get absorbed into the ballast. The reason why I apply the ballast in two (and sometimes three) layers, is because I have found that if you do the whole thing in one big layer, the bottom layer never really gets soaked with the glue mixture, and it will start to crumble over time.