apex-save-orgwide-custom-metadata-setting.cls

public with sharing class MyCustomMetadataHandler {

    @AuraEnabled
    public static Boolean saveDefaultDecimal(Decimal value) {
        Id orgId = UserInfo.getOrganizationId();
		List<My_Custom_Metadata_Default__c> defs = [SELECT Id, SetupOwnerId, Percentage_Value__c FROM My_Custom_Metadata_Default__c WHERE SetupOwnerId = :orgId];
		Database.SaveResult defSave;
        
        if (defs.size() == 0) {
            My_Custom_Metadata_Default__c nd = new My_Custom_Metadata_Default__c(
                SetupOwnerId = orgId,
            	Percentage_Value__c = value
            );
            defSave = Database.insert(nd, false);
        } else {
            My_Custom_Metadata_Default__c def = defs[0];
	        def.Percentage_Value__c = value;
        	defSave = Database.update(def, false);
        }
        return defSave.isSuccess();
    }
}