Render layer transparent

I am making a SNES system and using 2.62.Doing a test for the glare. I dont know too much about composting so not sure if this happens a lot or not. I have the snes system on first layer and the LED power light on the second. The light is transparent.I have it as a tube but light should be coming out from end. I could just resize the size but I would like to know whats wrong here for future projects.

Sorry to bring this up again but am I the only one that has this problem? There is knowone else out there that doesnt have objects render through other objects with cycles?

Either plug the led layer’s alpha channel into the factor of the mix node or use an alpha over node instead of the mix node.

To get a transparent sky in Cycles, go to Render -> Film and click Transparent. Note: this will apply to all your render layers.

Thanks guys for the help. Havnt tried any of that but Im sure one of those methods will work for me.

Another method (the one i would probably do), is use the zcombine node, which will combine the two objects based on their z-depth values