I use a small wireless keyboard to set things up. I also stuffed a U-hid nano from Ultimarc into a 2600 console so the switches work for navigation. I used a similar USB adapter for the controllers. I think I used Stella and not LR-Stella to make it work with paddle controllers too.

@loonyboi Thanks! I wasn't sure if you meant to mirror the controls by ES' UI or at file system level by copying their config files. So if I understand you correctly, setting them up identically in ES does suffice.

I'm having the same problem where none of my controllers are working in game, however, I know what you're talking about, as I had that same thing (with the having to basically hold all the buttons to get it to open the remap screen) happen to me. Unfortunately, I have no idea what caused it, and I was only able to fix it by doing a clean install. If it's any consolation, since the install I haven't had that problem (just my current one where my controllers aren't working in game)