The Markup tool () in SketchUp for iPad uses the iPad's native Markup capabilities. This means that when you activate the Markup tool you'll see the iPad Markup toolbar appear at the bottom of the screen.
With the Markup tool you can draw or annotate your model. If you aren't familiar with the options in your iPad's Markup tool, you can get more information here.
Once activated, you can use the Markup tool to draw nearly anything on your model. It's great for leaving a note for a collaborator, adding a contour to a surface to see what it looks like, or just suggesting a change. When you're done using the Markup tool, you'll tap Done at the top of the screen, saving your annotated model as a Scene.