Some users have IntelliJ modules that correspond to different git repos, Jenkins jobs and SonarQube projects. One can also link any local folder as a module (with 'Add Content Root' in the Project Structure menu)
It would be interesting to bind these modules to SQ projects, as they have possibly different QPs and settings.
See for example: Settings -> Build, Execution, Deployment -> Compiler -> Annotation Processors
Also related, when opening the parent folder of a project: https://groups.google.com/forum/#!topic/sonarlint/JfuwA3MjOZ4
(More generally, when opening the parent directory of multiple projects that are distinct projects in terms of SonarQube.)