Can I edit or manipulate the layout for the PDFs that are generated from submissions?

Unfortunately that is no possible, the PDF output format is fixed and not customizable.

An alternative would be customizing the e-mail message template instead. Then you can just print the e-mail message as PDF file (Chrome browser have this capability)

Hope this help, if you have another question non-related to this one, please open a new thread, we will be glad to assist you.