Does the Snyk CLI support monorepos?

I have run Snyk monitor against two files in my project but I only see one of them on the Snyk website.

Yes the Snyk CLI can be used against multiple target files within the same project, but we need a way to differentiate between each file, otherwise we think of them as the same Snyk project. 

To differentiate them use the --project-name  flag.

For example> 

snyk monitor --org=myOrgName --file=package.json --project-name=myapp-frontend
snyk monitor ---org=myOrgName --file=build.sbt --project-name=myapp-backend

Note: The project names you set need to be unique across the whole of your Snyk organisation.