This question is in reference to Atlassian Documentation: Setting up your workspace
In the example you set the project to be the actual team name. Is this how you would recommend a small organization with 1-3 teams set up their work? Do the actual 'projects' then become Epics? I am the Agile Coach for a small organization but trying to lay the foundation so we can easily grow into a larger org that leverages SAFe. I know Rally like the back of my hand but am new to JIRA so defining the proper team object and then allowing multiple teams to work on a single EPIC would be ideal. I would like a single backlog per team versus making my PO search multiple 'projects' in order to prioritize work for one team. Any help is appreciated.
You may like to have a look at https://www.atlassian.com/agile for lots of links and pages on how to do Agile on JIRA. When it all gets too much it is worth having some light relief with the videos on Chet Rong - the worlds worst agile coach. https://www.youtube.com/watch?v=HsB0UZR7XvE&list=PLypC2fA0xsaWULkC3Q9b1dXdZGIi0oj-h
Now to talk about some of your points in more detail. As you have seen JIRA is configurable in many different ways!
From the way you describe your organisation I would approach in the following way (but this is only one of many possible approaches). As this gives you a way to scale as you need to.
I hope this helps and if you can provide more information on your business requirements then I am sure others will also have opinions and other options for you.
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