If you name the emulator Retroarch then you only need one entry for it, you just go to the associated platforms tab and specify the core you want for the particular system. If the system is not listed there you can simply enter it at the bottom of the list. Also the system names used in the associated platform list must exactly match what the system is called in the left sidebar in Launchbox in order to work.
Also if you have changed the emulator for a platform you need to bulk edit the roms to use the new emulator. Click on a game in that platform and use ctrl A to highlight all the games, right click one and go to edit, this will open the bulk edit wizard. Click next,then in the dropdown pick emulator, then in the second dropdown that spawns choose the emulator to use and finish out the wizard and launch a game.
EDIT:
The reason you only have the one entry in the associated platform tab in your image above is because Launchbox doesnt know that it is Retroarch, so i suggest naming it that and that associated platform list will be pre-populated, like this.