Snyk will automatically detect your pom.xml file in the root of your project. However, each pom.xml in a multimodule project is represented as its own project in Snyk.
So if you're using the CLI, this means running
snyk test and
snyk monitor separately for each pom.xml file.
If you're using the Github integration, add the repo to Snyk, then add submodules from the project page by clicking on the + icon on the top right of the root project: