Perhaps I can clarify that to you...
jira.atlassian.com is used to search or create bugs, features, suggestions requests to improve Atlassian products.
name.atlassian.net is your website. Where you are going to create your projects and etc.
Please let us know if you have any other doubts.
Separate servers for different purposes.
Jira.atlassian.com is Atlassian's own JIRA installation used for gathering improvements, bugs and issues from users of their software.
yourname.atlassian.net is your installation of JIRA for your use. That's where you should work on your own data.
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