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Lots of good ways to do it. Generally, arrange them in the same way as you would deploy them. So a stack for EC2 is unlikely to be useful, since you'll have instances that you want to never re-deploy, instances that get deployed frequently, instances that might get deployed once or twice a year...
Often, people organize projects by purpose (e.g. "my main app", "the auth infrastructure", "the network and firewalls"...), and stacks within projects by scope (e.g. "dev playarea", "Europe", "staging").