Ok, I’m a total noob to retropie (apologies if my terminology is off) and I feel like I have everything working the way I want except for one thing.
I got Retropie working and when I would play a rom, the joypad would control the game and the keyboard would work as a keyboard (F1 would bring up help, ESC would exit the game, etc). Then I started to run into some problems and I decided to start with a fresh image of Retropie.
So starting with the new image, I loaded my roms from a flash drive and configured my joypad to work within retroarch by editing the cfg file in RetroPie/configs/all. I added a button combination to the config file to exit retroarch using the joypad. I also edited the config for individual emulators. Those last two things are the only things that I can think of doing differently from last time. Now when I play a game, my keyboard just works as another player 1 joypad. I’m sure I’m just missing one little thing. If somebody could help me out, I would really appreciate it.