I too created all my own art, game play, and will add sounds. I first started with the concept, then fine tuned the gameplay and controls using rough sketches for the character and obstacles, then cleaned up the artwork when I was close to finished the first few levels.
I've been using Trello to manage my game tasks and it's been working pretty well. I also use it in tandem with OneNote for drawings and more extensive notes. But Trello has been easy enough to use for task management and noting ideas when inspiration strikes, so you can keeping working on the task at hand. Also, re-sorting tasks is super easy. Try it out.