Just replace /site/modules/Padloper folder with the new version (remember to replace whole folder, don't just copy new files). Then do modules => refresh on PW admin and finally go to Modules => PadCart settings and insert email related settings there. These used to be inside shipping module, but now they are part of the Padloper-core.
Also you might want to take advance of new more streamlined checkout. Just change $modules->get("PadCheckout") into $modules->get("PadOnePageCheckout") in your checkout template.
Let me know if you end up having any kind of problems with your upgrade. I am here to help!