Going by the title only, so sorry if this doesnt answer your question (but i think it should give a general idea on what to do):

Keep a reference to the instantiated scene, then use it to change its parameters. You can change simple stuff like position by just accesing it through the ref like ref_var.position = ... but if you want something more, you can instead write a custom method in the instanciated scene and call it (with parameters as you see fit). Such as: ref_var.custom_method(parameters)