The way the smelter is used, is by mining different ores in a specific order, combining them into a new ore that's worth more. For example, if you mine Bronzium and directly after that Silverium, they will combine - so instead of 1 Bronzium and 1 Silverium, your cargo will now have 1 'Sterling Silver'.
Aether stone is created by the smelter by combining Lightning Stone with Unobtainium (looks like a black ball with small gems on it). Lightning stone itself cannot be mined, but is created by the smelter by combining Electronium (looks like a yellow lightning bolt) and Amazonite (looks like a blue gem).
So to create Aether Stone, mine the following three ores without anything in between: Electronium, Amazonite, Unobtanium.