Just down the bin file from the website and run it - the upgrade steps are self-explanatory as you go.
I have upgraded a lot of applications in my career and JIRA/Confluence seems to be the easiest and seamless.
Points to note;
1) Check your current version and the new version gap - if the gap is huge , try going to a version in between the two extreme versions.
2) To decide on Step1 , you need to go through all release versions to ensure that you know what you will be seeing after you upgrade and what you might not see in the new version.
3) Plugins - ensure that your new jira version supports all plugins/ requisite plugins that are running in your current JIRA Version.
4) Files that you've added as a part of your organization's JIRA Customization " could" get reset or modified - do validate them or place them back to see your customizations again.
EXPERIENCE - My experience says that you always run an upgrade on your test environment - even if you have prior experiences on jira upgrades because it helps you avoid committing mistakes during Production upgrades or at least helps you visualize as to what you can expecte after upgrades.
Software and Service Desk can be upgraded after you upgrade Core - those two can be directly upgraded via Admin Console.
Happy Upgrading.
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