Here's a description of what goes in each folder:

_tools - Any tools that non-coders can use to create data files.
audio  - Music Files. Split into BGM and SFX.
css    - Cascading Style Sheets. This will probably be used very little.
data   - Assets such as .tmx (Tiled map files) and JSON data/story files. .tmx files must be in the data/ directory as this is where Quintus expects them to be (FIXED).
images - All images files. Split into ui and sprites
js     - Most javascript files go here.
lib    - Any libraries that we are using.