Manga Studio 5 comes equipped with some great tools, pencils, pens, India ink, watercolor, and oil brushes, just to name a few. But knowing how to make custom tools can help speed your process along, especially if you find yourself doing repetitive tasks that could be left to a custom brush instead. An example of this is putting leaf texture on a tree. Instead of doing this by hand, you could customize a brush to create the effect for you. A few tweaks, a custom texture, and your tedious task just became a whole lot easier.
You can also create custom tools to mimic a huge number of traditional art mediums. If you like to sketch with a non-photo blue mechanical pencil, then do your drawing with charcoal pencil, and finally paint over the whole thing with acrylic paints. All of those steps can be mimicked using Manga Studio's coloring engine. It takes some patience, and some tweaking, to make your own tools. But once you get the hang of it, and get a library...