If I want to add in a lot more information to a particular box, is it possible to create a hidden “note” section where I can add more detail without cluttering up the flowchart?
Take a look at the following: https://about.draw.io/interactive-diagrams-with-custom-links-and-actions/
Recommendation: Define a new layer called "Information". Add textBox visually close to your object you wish to display text. Put the textBox on the "Information" layer. Add an object that looks like letter I or ? . Modify the URL of this object to toggle layer to also be on your primary display layer.