Did some searching online to see how others have handled organizing issues on GitHub for their own projects. This one by Robin Powered is by far the best I have seen so far. I have broken down the image in the blog post so that it can be easily copied and pasted into my own GitHub issue label manager and even put my own spin on it.
If the repository covers multiple parts, this is how we designate where the issue lives. (i.e. iOS and Android for cross-platform tablet app).