I have my assets folder structure like this
assets
javascripts
products
--product.js
--productValidate.js
store
--store.js
As far as I know assets pipilene is something that should be precompiled. So... conceptually it should take all files at once and return just one copiled file, and it is good for caching.
You can store them somewhere out od assets (in puplic, as older Rails do, for example) and include it in depending to current controller and action