what kind of controller are you trying to use? it has to be plugged into your computer before you open nestopia or it won't realize it's there. once you do that go to input and in the upper right corner should be the name of your controller highlighted in blue [mine says Logitech Precision]. if it's there then there also should be a blue highlighted "Pad 1" on the left side. It's ready to be configued. Hit "set all" then hit up, down, etc etc to configure (don't hit anything when it comes to turbo a and turbo b, just wait the few seconds) and you should be good to go. here is also a good reference for setting up nestopia:
I installed Nestopia through the official Debian repos (using Debian 12), i.e. sudo apt install nestopia. I also have one of those official Nintendo NES gamepads that have the Wii connector, and I have an adapter for PC for that.
df19127ead