Can anyone give me any advice on where to begin with a second hand ser-6500. I need to re programm it for my cafe but am getting nowhere with the manual.

good machines but very long in the tooth now!
turn key to s mode hold down third button up on the right hand side, plug machine in - will display h/w check let go of the button and wait for the regi-num to be displayed.
follow the book for initial set up
in case you decide to ofer table service suggest you select soft checks and allow clerk interrupt on the initial memory set up