On 1964, go to Plugins then Input Settings. Set your controls (Digital Pad controls is optional).
Recommended control settings:
C Buttons:
C Up=Home
C Left= Delete
C Down=End
C Right=Page Down
Analog Stick
Up=Up
Left=Left
Down=Down
Right=Right
Buttons
Start=Keyboard: Enter
A=Keyboard: X
B=Keyboard: C
Left Trigger=Keyboard: A
Right Trigger=Keyboard: S
Z=:Keyboard: Z
These are the controls that are automatically set up in Project 64. In 1964 you'll have to set it up yourself, so I used the same controls I did with Project 64.