How to make skybox transparent.

Actually you don't need to make the skybox transparent. What I think you really need is THIS. It will allow you to display only specific elements from a camera.

Personally I use this trick when I want to display some elements at the same place of the screen at anyh time for a first person shooter for example : a camera follows the player, and another displays only ammo, used weapon, ... The second camera displays only a specific layer and nothing else.