A newly-installed, fresh JIRA instance comes with a lot of default schemes for issue types, workflows, field configurations, and permissions. These default configurations are suitable for simple bug tracking and have a process that is applicable to any generic project. Don't be tempted to start customizing the configurations too soon. If JIRA is being used for the first time in the company, then it's a good idea to pilot it with default configurations. This will give users a good idea of what JIRA has to offer and collect feedback from the users.
When you are ready to customize configurations, either start with the blank configuration, or create a copy of the default configuration and then make your changes in that.