Leave stencil in place. There are many color mediums that you can use. Remember to start with the lighter colors, working to darker as you go. Also, work from the outside of the stencil to the center, as this will produce the desired shading for borders, etc. If you have a specific design i.e. apple, butterfly, etc., you will want to determine where you want the darker shading and work accordingly.
Ink-pads: These often produce a more delicate color and are great for certain effects. You can apply with either brush or finger dauber. The dauber works great on larger areas to just "pounce" on the color. Remember to work out excess color on paper towel before applying to stencil, whether using brush or dauber.
Paintstiks™: Paintstiks are an oil-based paint in solid form. They come in both regular and iridescent colors. When new or having not been used for sometime they will develop a "skin" on the surface. Use a paper towel to rub off the skin and get to the creamy consistency of the paint. Place a piece of wax paper on your work surface and stroke the paintstik across the wax paper in order to have a "palette" of color from which to work. Using a stencil brush, pick up color, work out excess on a paper towel and use a dry-brush technique to apply the color to stencil. Dry brushing means that your brush has very little color left in it and the buildup of color will be determined by how much you brush over it. Work with a circular motion from the outside of the stencil, lightening the color as you reach the inside. This will develop the shaded effect that makes the designs so attractive.
Chalk: If chalks are new you will need to scrape the chalk to get it started. This is a relatively easy medium to work with, however you need to be careful not to let the chalk dust build up around, or sneak under, the bridge of the stencil as you work. Pick up color on your stencil brush and work with a circular motion to apply. You can finish this off with a thin coat of Dreamweaver translucent embossing paste while the stencil is still in place. This will give a nice shiny look to the finished product. Or you can spray with a craft finishing spray, or even with hair spray.