I can drill holes with a manual drill but I’m going to be more efficient with a power drill. Switching from a manual drill to a power drill does not change the fact that I’m a skilled carpenter.
The same holds true for JIRA. It is a tool. The people using JIRA should already have processes and procedures for how they do their job. When I teach Kanban, XP or Scrum I don’t use tools like JIRA. I might use a physical wall and index cards. Once the team knows how to do the work, we introduce tools like JIRA to make it efficient. How we configure JIRA depends on how they are going to do their job. So understanding how the team does the work is key to how to configure JIRA.
JIRA is highly configurable. There are many third party plugs which will make it more efficient. You just want to avoid having the tool define (or re-define) how they do their job.
The biggest danger of JIRA is that it is highly configurable. The second biggest danger is not paying for third party plugins. Sometimes the out of the box JIRA doesn’t do exactly what you need. You can make it but it is sometimes easier to buy a plugin rather than spend weeks trying configure the basic JIRA.