This thread should give you the information you need:

http://forum.unity3d.com/viewtopic.php?t=33679

Basically, you can get the scene camera with Camera.current, but you NEED to check if it's null, since that variable is only available when the Scene view has focus, otherwise it will be null.

I'm not sure how much you can modify the Scene camera, either... I've heard mixed reports in the past. I've heard you can't really change how the camera behaves very much, but I've also seen some editor scripts that (claim to) modify it, so if something isn't working for you, it might just not be possible.

I had the same issue and wrote a script that follows the specified target transform. It even works for multiple SceneViews. It's on Unity3D's wiki now: http://wiki.unity3d.com/index.php/SceneViewCameraFollower Hope it helps.

There is another way to accomplish this using the (undocumented) UnityEngine.SceneView interface. While there is no way to directly set the current scene view camera's transform, there's a handy AlignViewToObject call (identical to the GameObject menu item). Here's some C# trickery:

var view = SceneView.currentDrawingSceneView;
if(view != null)
{
    var target = new GameObject();
    target.transform.position = NewCameraPosition;
    target.transform.rotation = NewCameraRotation;
    view.AlignViewToObject(target.transform);
    GameObject.DestroyImmediate(target);
}

I use this general strategy in a number of ways to make scene navigation less painful for myself, but you can probably see how it might be altered to suit your needs (e.g. since you are updating the camera every frame, it probably makes sense to keep a persistent dummy object around for alignment, rather than creating and destroying one each time).

Hope this helps!