How can I set the position of a mesh before I add it to the scene in three.js

I would recommend you to check the documentation over here:
http://threejs.org/docs/#Reference/Objects/Mesh
As you can see on the top of the docu-page, Mesh inherits from “Object3D“. That means that you can use all methods or properties that are provided by Object3D. So click on the “Object3D” link on the docu-page and check the properties list. You will find the property “.position“. Click on “.position” to see what data-type it is. Paha..its Vector3.

So try to do the following:

// scene is an instance of THREE.Scene
scene.add(mesh);
mesh.position.set(100, 100, 100);