welcome to PeerfactSim.KOM. The location for new classes doesn’t matter for the functionality. But it is easier and more readable if you use same structures as they are there at the moment (for example a components package for each overlay).
As the simulator is implemented in Java it is necessary to have a basic knowledge in Java to implement own overlays. As good starting point you can look at the other contained overlays. They already offer different kinds of services and implementations for different purposes