To annotate (highlight text, add notes) to a PDF, you will want to activate Paperpile's beta Google Chrome extension in your Settings. To do this, first go to your Paperpile settings:
Then, go to "Browser Integration" and select "Viewer with annotations (beta)" choice in the drop-down:
Once you have activated the beta PDF viewer in Google Chrome, select a section of text in any PDF in your Paperpile collection. You will see your options to Highlight that text. Click the box dropdown to add a "text box" to any place on your PDF page. You can then add comments to that PDF that are then saved in the PDF.