I know the basic overview of them, but what is the practical scenario for each of them?
As cfn-init used to bootstrap the servers and SSM helps to execute the commands via ssm documents.
Difference between cfn-init and SSM?
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As you said, cfn-init is used to bootstrap a server when it is initially created.
The Amazon System Manager is used to maintain a server afterwards. System Manager can be used to ensure ongoing security patch compliance, install software updates, run ad-hoc commands, etc.