It doesn't.
Atari 5200 controllers aren't implemented at all. There is no analog input into the system.
If you use something with analog, it's converted to digital first, which is why so many games don't work properly (Super Breakout, Missile Command, etc)
Basically it's an Atari 800 emulator (Which had digital 2600-style joysticks and a keyboard) with some 5200 stuff slapped-on.
If you have a keyboard attached, Numbers work from the keyboard. For instance, LEO in countermeasure is 123.