Hi Tim,
There’s no one way to do this but our generally recommendation is to use different Atlas Projects within your Organization for these different environments. In each project you’d then have a different cluster (you might use a much smaller cluster for dev, and maybe you frequently pause your test cluster, etc).
Projects offer security/authorization level isolation (e.g. which team members have access) as well as isolation of configurations like Alerts which make them ideal for separating Prod from non-prod environments. A common pattern is to restore a backup from prod to a non-prod environment for test purposes. https://docs.atlas.mongodb.com/best-practices/#the-project-level may be of use.
Taking a step back, I love the question because it’s good for thought for us to figure out how to make it easier for users to set up best practices.
Cheers
-Andrew