I mostly use embedded views for reusable components, but be aware that they come with a performance cost, especially if you go multiple levels deep. There's a good discussion about this here.
For folder structure, I typically nest /Embedded and /Popups within my main view folders. My projects all inherit from a Master project that has a root UI folder where I store all the reusable components.
Every project has a corresponding development version where I do all my building and testing before exporting changes to the live version. They use the same name, but lowercase and starting with an underscore, so I develop in _master and deploy (export) tested changes to Master.