Yes, Ponder does work with PDFs! If you visit a PDF in your browser with Ponder installed, anywhere on the internet, it will be invisibly converted so that you can create responses on it just like any other web page. It will even work with scanned PDFs, so long as they have been text-converted. (More info from Adobe on using that feature of PDFs.)
If you have specific PDFs you want to use for your class, you will need to make them available somewhere accessible with a browser. For example, on your school's Learning Management System (LMS) or other class web site. If you don't already have a place online to share documents with your students, you can create free accounts to do that with either Google Drive or Dropbox.
These articles provide step-by-step instructions for sharing PDFs with each:
Once you are able to browse to the PDFs, you will want to add links to them to the Ponder Course packet for your group.