The configuration document should have information about all the schemes, along with the relevant background information to justify it.
This document should have the following sections.
First, start by asking these questions: what kind of issue tracking is required in JIRA? Do you want to keep track of your customer complaints or track bugs in your ongoing project? You may be tempted to start using JIRA and customize it on-the-go, but this approach will lead to a messed-up system in the long run and will be difficult to manage.
Once the purpose of using JIRA is clear, identify what kinds of issue need to be tracked. If JIRA is going to be used for simple bug tracking, then the existing issue types are sufficient, but if you want to use JIRA for support tickets, then you might want to create new issue types.