StaffPad Reader has a very unique approach to annotations. Once you understand a few basic concepts, it's very flexible and very intuitive.
If you have an Apple Pencil or Windows Ink pen, just start writing with it on the page...
If you don't, you can use your finger to ink. Press the "markup" icon 
on the toolbar to reveal the markup bar. From here you can choose which of the three pens to work with, and also erase individual annotations with the eraser icon, or delete all your annotations at once by using the 
trash can icon. If you make a mistake, use the undo and redo icons.
By default, annotations are made in red pen. This is a private pen. Anything you write with the red pen will only be seen by you. Use this for your own annotations that you don't wish to share with others.
The yellow highlighter is a private pen as well. Only you will see this, and it can be useful for just bringing your attention to certain areas of the score without obscuring anything.
The grey pen is a public pen. This means that any ink strokes you make with this pen are sent back and visible to StaffPad, as well as to other Readers on the session. This can be very useful if you are the section leader and want to mark up bowings, for example, that the rest of the section viewing the same part can see. Also, if you need to correct or communicate with the composer or conductor using StaffPad, you can write in grey and they'll see it in position on their score.