I have no idea about plugin for CocosBuilder. So let some expert comment on it.
For managing resources:-
You can create multiple folders like this:-
// For iOS
You need to create these folder under folder: ccbResources
Also by default the CocosBuilder pick resources from ccbResources folder instead of resources-iphone. It simply ignores resources-iphone folder. But for the rest of resolutions, it picks resources from their respective folders.
Let me know if you face any problem.