I just downloaded the latest "stable release" of the stella emulator (ie: stella-2.3.5-win32.zip) from here:
http://stella.sourceforge.net/Once you unZip it you will see a "Docs" directory which has an
index.html file located inside. View this HTML page and then read section 8 (Keyboard Layout) and then section 9 (Event Remapping). I believe section 9 will allow you to remap the keys to how you want them.
Just double-click the "stella.exe" which should result in a window popping up. Click "Options", click "Input Settings" and then scroll down to "P0 Joystick Fire" (for some reason player1=P0 and player2=P1). Anyway, you can change the key mapping there if you want it to be something else.
** Actually it seems the default key mapping for P0 Joystick Fire is "SpaceBar"
or "LCtrl" already, so if you can simply use
LCtrl you might not need to reset any key mappings then.
Anyway, stella is pretty powerful. A lot of nice options in the index.html file you should read through if you to tweak stuff .
Good luck