Well, the scientific answers to your questions are something like this...
(1) "Empty space" isn't exactly empty. On average, there's something like 1 atom per cubic centimeter (or something like that). Plus, there's energy associated with space and there's also the sudden appearances/disappearances of virtual particles. Einstein's theories may also indicate that space (or "spacetime" is essentially the same thing as gravity, which is essentially everywhere). So yes, "space" is different than "nothingness" etc.
(2) Yes, the Big Bang created space. And time. The 'kernal' was not sitting in empty space at all. But there are some speculations that the 'kernal' was an aspect of some kind of quantum foam (a virtual particle kind of metauniverse)...but that's just a educated speculation because there is no way to scientifically test what is 'outside' or 'before' our spacetime (the very question may be nonsensical...kind of like Hawking's question of 'What is north of the North Pole?')
(3) Science does not know what is in the singularity of a black hole. A new branch of physics is needed to explain this phenomenon (probably one that can combine Relativity and Quantum Mechanics...or maybe String Theory).