Workflow

Check out "Understanding the GitHub Flow". Don't worry about overwriting master, it's a protected branch so all pushes have to be reviewed by someone first. Make new branches for each feature/fix you're working on, and commit/push regularly. Open a pull request on GitHub when you're ready to merge back into master

Agile tools

Install the ZenHub extension for your browser. This gives you built in "Boards" (a Kabana board) and "Reports" (burndown, etc) tabs.