I'm using Afloat to give me the "always on top" feature on every application window.
I can't find Afloat's settings.
I can see in the Window menus of my other programs, but I can't find its app or its settings.
There really are no preferences. I checked the installer bundle and there really is nothing in it except the SIMBL installer and SIMBL bundle providing menu items, so no System Preferences pane or standalone management application. And since there's no menu item for configuration provided by the bundle, there's really nothing else. The documentation doesn't mention any preferences or configuration either.
I have an ancient preferences file (from 2007) on my system,
If you want to customize the keyboard shortcuts, you can do so in System Preferences » Keyboard » Keyboard Shortcuts » Application Shortcuts.