Ok, so what happened was..... with the SNES and NES roms I had left them in their zip folders. And the emulators seem to handle that just fine. But apparently the Atari and the Apple2 emulators don't recognize the zip folders. Yes, I know that's a beginner mistake, but my previous knowledge is zero.....so...... And now I know what it means on the github documentation that the accepted extensions like .ATR etc are specific for the destination folder. I am so new at this I didn't even know what to look for. But I'm reliving the 80's like a boss now.
Thanks again for your help, y'all fixed it!