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 one of the four colors 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, type your thought and choose Save note. 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 or your finger; a mouse works too. Pick a color and one of three widths, or switch to Erase 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 in the order you made them, each marked with its page number. Click any entry to jump to it, or delete it from there.