When you go into the "Administration" (link is next to your name in the upper right of the screen) for JIRA, on the first page you will see a summary of "Projects", "Plugins", "Users", "System".
In the section called "Plugins" you will see smaller sections called "Plugins", "Application Links", "Source Control", "Builds", "Agile". In the Agile section you should see a option there for "License Details". Click in there to enter you license. It also has a link to your "My Atlassian" page in case you haven't downloaded your license yet.
I'm assuming here that you are using JIRA 4.4.x. If that is incorrect, let me know and I'll provide instructions on the old way (if I can remember them).
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