oh dear....
choose options/setting from the PJ64 menu, select N-Rage Plugin 1.61 as ControllerPlugin.
then select options/configure Controller plugin. Choose MemPak(obviously) for Player 1, make sure RAW is checked, and type a name for the MemPak in the field on the right.
Now start PJ64 and realise Perfect Dark wont get far with PJ64 1.3, u have to wait for the realese of 1.4 anyway