I can't see the 2nd layer rendered in the Compositor I have been following BlenderGuru's Create a Spaceship in Blender tutorial.
So far so good, until now when doing the compositing.

I believe I have followed every step he mentioned, I have also revised them a few times. Yet when I change the ID Mask's Index (as he does), nothing changes on my screen. 
I did assign the Material Pass Index to the material that will be glowing, which is on the 2nd layer. The Render layers are correctly setup, with the main layer set to create the Mat Index pass.

But instead of getting something rendered in the 2nd layer (so it can become the glow eventually) I only get a totally black or white screen.

Note Price only uses 1 render layer node. And only the main scene layer is enabled when rendering. Somehow this works for him.
I have been advised to use 2 render layer nodes instead, and to enable both 1st &amp; 2nd scene layers for rendering. This alternative method does work to some extent, as the 2nd layer gets rendered. The problem is that you end up with the glow behind the box, when it should be over it.

If you go to this specific time in the video you'll see while he's creating the Render layers, he only needs to identify the Render layers, but the Scene layers stay the same, which is only #1 (where the spaceship is).

Anyway, you can inspect my test file should you want. nopass_02.blend. This one is the one like Price's, with 1 render layer node.  

Here's the other one with the alternative method, with 2 render layer nodes.
The alpha over node uses the box's alpha (donuts are inside the box)

so it mostly covers your glow effect (white alpha will be over the other image). If the desired effect is what I suppose, i suggest you to use an Add node. (light is added)