Find the structure first
Before reading a long PDF cover to cover, open its outline or table of contents. Identify the chapters relevant to the question you need to answer. If the file has no bookmarks, search for heading words, figure numbers or terms from the assignment.
Keep the printed page number
A reader may show its own page index while the document has a different number printed at the bottom. When citing an article or textbook, note the page number that appears in the actual document. Reflow modes can change what is visible on each screen, so they are less reliable for exact references.
Read with a question in mind
Write one question before each section. Highlight only the sentence or evidence that answers it, rather than painting every paragraph. A short note such as supports claim about memory, page 42 is easier to use later than a page of unexplained highlights.
Test the file's text layer
If search returns no results for obvious words, the PDF may be a scan. Selecting text is a quick check. OCR may help, but mistakes in tables and mathematical symbols must be corrected against the page image before you quote them.
Create a way back
Save bookmarks for diagrams or definitions you will revisit. Confirm the PDF still opens at the same location after you close the app. Export your own notes if possible; do not assume replacing the reader will preserve its internal annotations.
For your next study session, open the PDF in Readream Basic and bookmark the section you need. Work through a short part before adding marks across the whole document.