The plugin configuration is quite simple. You can setup your SonarQube settings in your JIRA project settings section:

There are five options:

• SonarQube Server URL: this is server base URL for your SonarQube installation
• Token: this field is optional. If your SonarQube instance is not public, then you will need to setup this field with the security token from a SonarQube user. You can find more information about SonarQube tokens here: https://docs.sonarqube.org/display/SONAR/User+Token
• Resource ID: this is the key of the SonarQube resource where you are going to retrieve the quality metrics. You can get this key from your SonarQube project dashboard or your sonar-project analysis parameters. 
  • Note: since version 1.4 you can setup more than one resource/project key by providing a comma separated list of resource keys. Measures will be aggregated into a unique view of all the projects together. See section linking multiple projects to Jira.
• Issue type: This is the default issue type to create new SonarQube issues
• Custom metrics:  List of custom metric keys to display in the dashboard, you can specify 1 or a list of metric keys separated by commas. For example: blocker_violations, major_violations, classes. Check with your SonarQube administrator to find out the keys to the available metrics

GLOBAL CONFIGURATION

You can configure a global server to use from Jira projects.

There are two options:

• SonarQube Server URL: this is server base URL for your SonarQube installation
• Token: this field is optional. If your SonarQube instance is not public, then you will need to setup this field with the security token from a SonarQube user. You can find more information about SonarQube tokens here: https://docs.sonarqube.org/display/SONAR/User+Token