I have an application which is developed in Symfony2. Now the structure for it is as follows:
Like Elnur said, use one AppBundle is a good practice.
A single bundle implements the MVC pattern himself so i think it's not a good idea to use bundles to separate your layers.
I think the best way to use bundles is to think "open source". If the feature you are developping is enough generic to be released for everyone, or to be reused in a future project, place this feature in a bundle. This way will force you to build the feature without any business rule which belong in your AppBundle.
Bundles are bricks