You can copy the main inputconfiguration.sh config script and then modify the path where the configuration scripts are, pointing to your own script folder (i.e. the Dolphin mapping script). You can run the script manually so you don't have to go through EmulationStation each time you want to run your mapping script.

To get more details when running a script, use either bash -x <scriptname> to see a step-by-step execution trace or modify the script header (1st line) to use bash -x for execution