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
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.