unfortunately, it seems that currently launchbox has no option to run the emulators exe files with the custom configs being set by emulators, nor the option to use the config files created by some emulators to import these settings and make lauchbox use them when launching an emulated game. maybe this feature will be added if requested by the community.
However, there is a workaround, you can launch an emulated game with whatever configs there are, by simply specifying the app path as the emulator exe file. then, in the command line parameters, put the full path of the iso file of the emulated game, including ".exe" with the file name, example: "C\Games\Uncharted.Iso" with the markers. this way launchbox will launch the emulator with its specified configs for each game that has been applied in the emulator itself.