I would like to be able to configure CUPS-PDF (at
http://localhost:631/printers/Cups-PDF) so that I can choose the
location to save the PDF file (presently it saves all printed files to
desktop by default).
Adding my user name to the sys row of /etc/group enabled me to modify
the settings at the above page, but there was no option to modify
output location to save the PDF file.

Any suggestions for the above problem ?

Thanks,

Jay

Edit /etc/cups/cups-pdf.conf , specifically the line starting Out
(under Path Settings). You'll need to be root.