Hey Stephen, the workflow can definitely be a bit tricky but hopefully we can help clear things up. The workflow that I have is:
1. Create the animation
2. Render out a single test frame (could be lower quality than the final render, and you don’t need to save it outside of blender)
3. Composite based on the test frame
4. Render out the image sequence (your compositing will be applied to every frame)
4. Combine sequence to create a final video
The compositing will be applied to every single frame before it’s saved to your computer, so in a way you are running it through a pre-configured setup. The one or two single frame test renders will be enough to tell you what adjustments are needed.
Does that help?