As with any other software project, treat your JIRA customization as a project in itself. As a JIRA administrator, you should first meet all the stakeholders to understand how they want to use JIRA. This usually starts with a brainstorming session with all the teams' managers.
When you want to start customizing JIRA, always prepare a document to store all the configurations that are required. Even after implementation, if any further changes are required, you should still update this document. This also helps a new administrator take charge of the JIRA instance. When all the requirements are stored in the configuration document, then it is much easier to track the changes that were done in the system. If you already have a Confluence instance running, you can use it to create these documents, which can be accessed by all the stakeholders. Usually, people use Confluence along with JIRA to collaborate on documents and share information.