Currently I am using Node.js for the backend and either extjs or backbone for the client and I am now completely confused on the folder structure.
Using express
Just put the whole /webapp
under /public
so you'll end creating, for instance, frontend's models under /public/webapp/models
appname
|--models
| |--appmodel.js
|--public
| | |--webapp // extjs/backbone files
| | | |--models
| | | |--controllers
| | | |--css
| | | |--js
| | | |--img
| | | |--views
| | | | |--appview.ejs
| | | | |--extbasedview.ejs
|--routes
| |--router.js
|--app.js