Theme Engine Documentation
What is the files structure?
Layout files are stored in the computing servers, separately from the static files (images, CSS, etc.). How to access static files you can learn here.
Static files get sorted to 3 directories (/css, /images and /fonts). Then these 3 directories are uploaded to the Content Delivery Network and sit together. So to access an image from a CSS file you should go one folder up from the /css folder (../) and then to the /images folder. For example, you may access your logo here: ../images/logo.png.
No other file types than css, images and fonts are accepted. If you use JavaScript, it should go with a corresponding module, not a theme.