Everything you mark up is saved to the source, so it's there whenever you come back.
Highlight a passage
Select text in the PDF and pick a colour from the bar at the bottom. The highlight stays put, even when you zoom in or out.
Add a note
With text selected, choose Note and type your thought. Highlights that carry a note show a small marker — click it to read, edit, or remove the note.
Draw with a pen
Click the pen button in the toolbar to switch to drawing. On a tablet you can use a stylus; a mouse works too. Pick a colour and width, or switch to the eraser to remove a stroke. Click the pen button again to go back to selecting and highlighting.
Find everything later
Open the annotations panel (the panel button in the toolbar) for a list of every highlight, note, and drawing, grouped by page. Click any entry to jump to it, or delete it from there.