You can set the default save path and file type by changing the following Firefox about:config preferences:
The following is an example of the value that I use:
The headers and footers are set in the options tab of the print dialog. By default, these settings stick from session to session.
As an aside, I have compared the output created by cups-pdf and by the Firefox print-to-file pdf option, and cups-pdf produces clearer output and smaller file sizes on my machine. Also, PDF documents created with the Firefox print-to-file pdf option do not print reliably for me. So, you may want to try both to see which works best for you.