Is there a way for Retroarch to make my remapped inputs the default for certain cores?

Sorry if my title doesn't make sense, I'm still fairly new to Retroarch.

I'm tired of constantly having to remap my buttons for NES and Turbografx-16 games whenever I restart Retroarch. Even though I save the remap file and then save the new configuration, it still goes back to the default inputs. So is there a way to make it so it will load Retroarch with the custom remapping for certain cores?