No surprise, there is no cogent way to work with color in After Effects. If you have thousands of layers, in hundred of composition, across multiple edits, you are on your own. It’s no wonder people like Sander van Dijk put their own tools up for sale. Sander’s Ray Dynamic Color is arguably the only practical way to manage color in your work.
The good news is that Sander van Dijk is an After Effects master, and is asking you, the Ae using public, what kind of tutorials you want to see from him. You can request a tutorial by visiting this link.
Recently Sander has posted a look into coloring with his Ae plugin. The tutorial covers some of the ways that you can color elements in RDC, and what the differences are between those methods.
Ray Dynamic Color 2 added some new user-requested features such as import and export of the standardized ASE color palette file. You can learn more about Ray Dynamic Color here.