The colors are just a visual aid that you can use to give any meaning you would like to assign to them. Suppose you have epics from 4 different business areas on the same board, you can categorize them like that. We use them to differentiate between internal project, consultancy for customers and business development goals.
In order to change them, you could go into the backlog view of your scrum board, expand the Epics panel and click on the color icon:
Screen Shot 2017-01-14 at 16.34.09.png
Setting the colour used to be available through scrum boards only, but with the introduction of Kanban backlogs it has become available there as well on JIRA Cloud, given you enable the kanban backlog feature on your kanban board.
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