Oh, jeez. My planning is... not a mess, but definitely not streamlined either !
My current comic is outlined - essentially, from the least specific (what is each chapter about?) to the most specific (story beats, interactions, etc). That's the system that I find the easiest.
I have an app called ColorNote on my phone and computers that I use to make notes that come to me at inopportune times. It lets you color-code and search through by keyword, so it keeps my searching down.
I then use that outline to make thumbnails about 1/4 of A4 paper with dialogue and paneling. I do this part in pen, because it makes me be less detailed and "get to the point" so to speak, with visual shorthand. Everything has to be easy for me to read and blow up larger, since it's on paper.
Visual wise, I keep sketchbooks. I try my best to take photos/scans and back up the images constantly in case I ever have a hardware failure or flood damage. I use a set color palette for my current series because, well, I'm not great at color theory I started out with very basic colors for environments and then made skin tones based off of that, and all of these supplies for the comic(s) I keep in a designated folder.
Overall, I try to keep the most important things to my work locally (on my devices) or backed up in some other way. That way, even if the internet is down or Our Corporate Overlords have shut down service XYZ, I still have my files.
I'm not super sure I answered your question correctly, but I hope that it gives some kind of insight !