Open the game you want to use it on before copying over your saved data.
Try to open a saved game. This creates a .srm file associated with the game file.
Overwrite the .srm file with the desiredsave file.
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.
@matchaman if you use lr-nestopia you only use one button. L1. And you can map it to select. Select will still work the same. If you are in actual gameplay and you hit select it does not eject+ flip while you are in game. But if you say hit select once in gameplay when you get to the flip disk screen it will give you a disk side error. All you have to do is press the select button one time and it will correct itself. If in game you hit the select button an even number of times like 2x, 4x, etc... it wont give you the error. Not a big deal when you do get the error as you only flip a disk once or so while playing so you lose maybe a second of time. Again you need to switch to lr-nestopia as this does not work in lr-fceumm