Question: How do I clearly mark and label "To-Do"s directly in my code (using Atom on Mac) for later?

Answer: 
I'd just mark your comments with `# TODO`. Most IDEs have a way of aggregating these comments to a list. Atom is no different, although you'd need to install [a plugin for it](https://atom.io/packages/todo-show).
I use `input`s with a description of the surrounding code/what needs done, they stop execution to make it obvious something needs done while allowing you to continue.