You seem confused and you are interchangeably call mesos and marathon. Those two things are not equivalent. Marathon is run on mesos, but so you can run other things, many of which are not even containers.
Marathon is something on the level of kubernetes, although kubernetes is far more powerful at this point.
But you can also use mesos to run other things like deploy VMs (this is work in progress though), or actually run applications without using containers.
The kubernetes on mesos means that kubernetes can schedule on which agent each container will run on, but at the same time the mesos will decide which physical machines in your data center the kubernetes will run on.
Marathon is something on the level of kubernetes, although kubernetes is far more powerful at this point.
But you can also use mesos to run other things like deploy VMs (this is work in progress though), or actually run applications without using containers.
The kubernetes on mesos means that kubernetes can schedule on which agent each container will run on, but at the same time the mesos will decide which physical machines in your data center the kubernetes will run on.