You can add various types of annotations to your PDFs (highlights, notes, ink drawings, images, ...):
Open the document you would like to annotate.
Tap the annotation edit button in the main toolbar. This shows the annotation toolbar.
Select one of the available annotation tools in the annotation toolbar.
Tap or draw on the document.
Some related tools are put in groups depending on how much screen space is available. To change tools within a group, long press on a tool icon in the annotation toolbar:
Annotations are automatically saved back to the document when closing it.