@granderjoree
In retroarch you can adjust the fullscreen width and height, this will change the resolution of the app, It may help none in performance. The aspect ratio is the part that scales the emulators output, to fit in your screen, you can do whatever you want with it, pressing the start button on an option sets it to its default value, you can save options for individual games, in the games quick menu and then under options, save game options.
The run command when you start an emulation gives you some control of the hdmi output, you can change to Monitor modes, or HDMI, some of the modes will not work, You can even change to a 50hz refresh rate.
There are additional configurations for individual emulators outside of retroarch, in these config files you can usually change the emulators rendering resolution. You can access the configs through the network share, if you set-up samba on the PI.