The normal workflow to manage a repository in GitHub should be like below.

Creation of a new repo:

• Create a new repo in local machine.
• Initialize git in local repo with proper gitignore and readme.
• Push to GitHub.

Make changes in the repo:

• Create a new issue for the change. It may be a bug, feature request or some refactoring in the repo.
• Create a new branch from main branch.
• Change the code and test.
• Create a new pull request and let other people to review your changes.
• When review is done and it is ready to merge then squash all the commits and merge in to main branch.