Yeah, just to clarify and elaborate on what @keltoigael said, the user 1 binds you are referring to are in the general Retroarch settings correct? Because those are the "general" settings which are used across the ui and are the default for any core you launch. To change emulator specific controls you need to load a game in the core you want to change controls on then open the Retroarch gui (F1 by default) then as kelto said you go to the "quick menu" then controls, change them to your liking, then in the same menu is a "save core override" option, use it. That will save your changed controls for that core only, and leave everything else as you set it in settings/input/user 1 binds.