Since Domino Designer is based on Eclipse, one of the nifty advantages is that you can use some of the same plugins as vanilla Eclipse. That "some of" is a big caveat, since Designer's base isn't the latest Eclipse, so some plugins won't install, won't work, or will even cause Designer to stop launching until you manually remove them. So... proceed with caution.
The first thing you have to do is to enable Eclipse plug-in installation, which is something you've likely done if you've installed the Extension Library. You used to have to go into your workspace directory and edit a config file to enable it, but 8.5.3 made it much easier. There's now a simple checkbox in the "Domino Designer" section of Designer's preferences (the fuzzy fonts come from my fiddling with GDI++ in my VM):
Once that's enabled, you can go to File -> Application -> Install. On the resultant dialog, pick "Search for new features to install" and click Next. What you do next depends on whether your plugin is an update site you downloaded (like the Extension Library) or one that's hosted (as it seems most Eclipse plugins are). Since the one in question is Eclipse Color Themes, you can click "Add Remote Location...", enter in a Name of your choosing, and enter "http://eclipse-color-theme.github.com/update" as the URL:
After that, you can click "Next", check the boxes for the plugin you want, and "Next"/"Finish"/"Yes" your way through however many prompts it gives you before it's done. Then, after a possibly-necessary restart of Designer, you'll be able to find the configuration in the preferences: