The Stella emulator for the Atari 2600 has so many options that you may have overlooked one or two. For years I did as well, even the one that I now use the most. Besides the overall Stellas settings you can configure in the Options menu, each time you click on options while you have a game highlighted, it will load the Game Options for that PARTICULAR game. You can then modify those options and they will not affect other games in Stella. Here's how to get your 2600 games setup just the way you want each one.
For complete instructions and a walkthrough
watch the video below