Does this imply that Epics only live in the Portfolio project and only storys in the team project? Also, if I add on the Jira Portfolio module does that change this recommendation on how to setup at all?

[Mary Thorn]

This question is in reference to Atlassian Documentation: How do I setup JIRA and JIRA Agile for the Scaled Agile Framework?

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[Steven F Behnke]

Epics can live wherever you want them to. Ideally, they live within the query that the team is using to create their Scrum board.

JIRA Portfolio doesn't enforce any changes to most JIRA users and systems. It's pretty much just plug and play.