The usual way to monitor a Linux hosts with Docker containers is to install the Checkmk agent and the mk_docker.py plugin on the host system. The plugin collects informations about the containers as piggyback data. These checks can be made visible when the containers are created as hosts in Checkmk. Don’t give them an IP address, and select “No agent”.
If you run the Checkmk Enterprise Edition, you can use the dynamic configuration daemon instead of creating the container objects by hand.
Other than in earlier Checkmk versions, the mk_docker.py plugin does not try to run the Checkmk agent from the host in the context of each container any more. But if there is a Checkmk agent installed inside the container, it will be executed.
There is a good documentation on this topic: Monitoring Docker