One of the principles of IaC is that all changes should be represented as code for review and testing. This is especially important where CloudFormation is concerned.
After creating a stack for you, the CloudFormation service is effectively hands off. If you make a change to any of the resources created by CloudFormation (in the web console, command line, or by some other method), you're effectively causing configuration drift. CloudFormation no longer knows the exact state of the resources in your stack.
The correct approach is to make these changes in your CloudFormation template and perform an update operation on your stack. This ensures that CloudFormation always knows the state of your stack and allows you to maintain confidence that your infrastructure code is a complete and accurate representation of your running environments.