You are using for sure agile methods to manage your infrastructure or deploy code on your application-systems and maybe running automatically patch-management on them.
AWS EC2-instances can be also automated and this can happen at the creation point of each single instance.
AWS from the command line
If you are reading this post, nearly for sure, you have an AWS account.
The most default way to interact with the AWS products is over the Web AWS console, which is reachable over https://signin.aws.amazon.com
There are some other ways to access your AWS products like EC2 or S3 over the command line from any system or distribution of your choice.