- Create a cloud application with one web role containing the codebase and additional web roles containing only the Web.config for the multiple virtual applications.
- On ServiceDefinition.csdef, define the virtual applications for the roles as required.
- Set a startup task to copy the contents from the complete web role to each of the additional virtual applications. This will be executed at role initialization time, with administrator privileges.
This way your deployment package won't need to include multiple copies of the same artifacts, and the virtual applications will be set up when the role instance is initialized.