I understand exactly. I'm going through the same thing, always looking in his favorite places. And I still put out food for Stripes, since even though I'm an atheist as well I still think he might get hungry! Nike is adorable.
I'm sad, and I'm angry. I'm finally at the point where I'm not angry at the world, though. Snapping at everybody. Laying on the horn in traffic. It had to stop. Keep talking to Nike. Years ago I lost a cat under strange circumstances at the vet. I did something I never thought I'd do and contacted an animal communicator. He told me a bunch of interesting things, but the most interesting was this. I asked him whether Bridget was still in the house, and he replied, "You have a thick, fleece, burgundy or wine colored throw at the foot of your bed, and that's where she is." Lo and behold, that's exactly what I had. I still talk to all of them.
"Some of you say, "Joy is greater than sorrow" and others say, "Nay, sorrow is the greater." But I say unto you, they are inseparable. Together they come, and when one sits alone with you at your board, remember that the other is asleep upon your bed." Khalil Gibran