I have wrote the author of WebStorm about new project item customization, but they never reply yet.
About create a project in WebStorm:
1. Please download our engine package.
2. Copy and rename the template directory to your favorite name, such as “myProject1”
3. Copy Cocos2d directory to your renamed template directory. Then open that directory by your WebStorm.
4. Open cocos2d.js file, find “engineDir:‘../cocos2d/’, change it to engineDir:‘cocos2d/’,
5. Open index.html file with HTML5 compatible browser to run.