It's a bit not as organized as I'd like... but I separate by series and then have folders for each chapter and other things such as references, misc art, banners/covers, etc. In the chapter folder are folders for CSP, PSD, JPG/PNG, and vertical.
I name my files like ch01_pg01.
I back up almost everything onto my Google drive. I also have two external hard drives that I back things on to every once in a while. I have to do that again sometime soon. I always back onto the Google drive though since it takes seconds to do.