Markup is StaffPad's term for annotations, or sketching on the score in ink that won't be fed through the recognition engine.
Tap the Markup icon 
and start scribbling with your pen to add annotations to the score. The toolbar will rollover to reveal the command bar, which now contains a set of tools for you to choose from.
You'll notice theres 3 colours.
- Red Pen:
- This is a private pen. This means that only you will see these markings on the score. They aren't broadcast to the Readers.
- Blue Pen:
- This is the default pen in StaffPad, and is public -- i.e this is visible to the Reader. Use this pen if you want the musicians to see your markings. Very useful for bringing attention or adding more freehand details to a musician's instrument part.
- Yellow Highlighter:
- This is also a private pen, useful for bringing attention to areas of the score for your own use.
You can also toggle the visibility using the 
visibility icon, or delete all of your markup in one go using the 
trash can.
Remember!
You can only draw, edit or erase markup ink whilst the markup layer is active