@johnny5126 I am new to Vice having only installed it over the weekend.
The video tutorial above that I used to map my joystick encouraged me to Save current settings, Save hotkeys and Save joystick map each time I made a new mapping.
I followed this advice and when I looked at the Vice config files in /opt/retropie/configs/c64, I noticed that changes were only being made to sdl-joymap-C64.vjm and not sdl-hotkey-C64.vkm which was the same as when first created.
For your maps to the virtual keyboard, for example, you should choose Save joystick map for them to persist. You can check this by looking at sdl-joymap-C64.vjm and you should see a line like 0 1 0 5 Virtual keyboard.