You need to hit the "tab" button to open the menu. Select "Game Properties" and change the "Type" to "F6SC (16K Atari + ram)". Hit "Okay" then "Exit Menu". You'll have to exit the game back to the main Stella menu, but then when you select the game and start it, it will work right. This game uses the second controller to deploy the smart bombs - the "F" key. This is one of my favorite hacks - very well done. It has all of the elements of the coin-op version, without the level of "impossibility" where it gets to be mostly frustration. The controls are actually easier in the hack version, because in the arcade, a separate button-press was necessary for thrust; the joystick just changed the direction you pointed.
This was probably already mentioned on a previous page but I downloaded the most recent .bin (I think) and all I see when attempting to play this in Stella is the title screen, then the radar and one "citizen" at the bottom otherwise the screen is blank
I hope this gets you up and playing...