"aws configure" simple creates the credential file for you on your workstation or server in the file %USERPROFILE%\.aws\credentials. You type the credentials in, it puts them into the file on the local server. As far as I know it doesn't do anything else with the credentials.

You can edit it directly to do exactly the same thing. It's a regular file, holding AWS access key and secret keys.

In terms of security, having your credentials stored in a file on a workstation / server unencrypted isn't ideal. If your computer gets a virus or ransomware they could be lost or stolen. If this ever happens you should remove those keys in the AWS console and issue new keys once your machine is sufficiently secure again.

IMHO the risk is worthwhile if you need to use the AWS CLI, so long as your machine has good security practices. Basics like a firewall, virus / malware scanner, etc.

If you run aws configure set help you will see that you can supply settings individually on the command line and they will be written to the relevant credentials or config file. For example:

aws configure set aws_access_key_id AKIAI44QH8DHBEXAMPLE

You can also run this interactively to modify the default credentials:

aws configure

Or run it interactively to create/modify a named profile:

aws configure --profile qa

Note: with the first technique above, whatever command you type will appear in your history and this is not a good thing for passwords, secret keys etc. So in that case, use an alternative that does not cause the secret parameter to be logged to history, or prevent the entire command being logged to history.