I am making a RTS game where you build armies, and bases. Then go and destroy your enemies base/army. But I have ran into another problem. When your player is created their waypoint is set to the same waypoint as the building. How do I do this? I have seen how you can instantiate a script with properties, but I need to instantiate an object, and set their scripts properties.
Instantiate() returns a reference to the instantiated object. You can use GetComponent() and similar functions to find its components. From there, the particular configuration tasks will depend on what exactly you want to do.
You can see a few examples of this in Unity’s manual page for instantiate calls. The page in question especially relates to instantiating prefabs, but the concepts are very similar when cloning objects in general.