For painted projects that have lots of holes, I would use spray paint. Either an rattle can or an air brush system.
If you want different colors in different places you can mask off areas with tape. just be sure to dry completly between colors.
if you want to stain, you can dip the project in the liquid stain and let it drip dry. There are colored stains as well as the wood colored ones. Or something like food coloring or RIT dyes on a previous thread.