If you choose to load the rom from within retroarch, you can either:
A) Select “Load Core” from the main menu, load the core, and then load the content.
OR
B) Select Load Contentand load the content of your choice, and a list of supported emulators that you have downloaded will appear, for instance… if you choose Super Mario Bros. And have Nestopia and QuickNES installed, it will ask you which one to use at the time.