Read about theming to create your own theme. If what you need is just to append files and folders to your drupal theme without altering it, you must create your own module for your application functions (if you have any), and add your script or styles files with calls to:
drupal_add_js(drupal_get_path('module', 'yourmodulefolder').'/path/to/your/js/file') drupal_add_css(drupal_get_path('module', 'yourmodulefolder').'/path/to/your/css/file')
You can add these calls in any hook in your module (I take the dirty way: I put this kind of lines in the global scope, althought it's not the better solution, it doesn't break what I'm doing).