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 this question, 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.