In classical mechanics the zero point of energy is arbitrary - and consequently the distinction between positive and negative energy is arbitrary.
Recall a ball near the surface of the Earth has potential energy approximately m*g*h (m=mass, g=acceleration due to gravity=9.8m/s^2, h=height). Where do we measure the height from? The ground? The center of the earth? The table the ball is sitting on?
It doesn't matter! These will all give different potential energies, but only differences in energy are physical.
That being said we conventionally for gravity and electrostatics we take the zero of energy as when all the particles are infinitely far from each other (because potential energy drops off as 1/r).
So for example consider the sun and Earth system, this has some negative gravitational potential energy, -E. E is the energy that would be released in moving the Earth from infinitely far away (through free space) to its current distance from the sun.
Conversely E is the energy that would be required to push the Earth out of the sun's influence.
Now consider an isolated H-atom - it is a bounded system. The electron is bound to the proton! (In a very similar way to how the Earth is bound to the Sun). What you would call the total energy is the energy released when we add an electron to a proton to make Hydrogen. Conversely it is the energy required to rip an electron away from the hydrogen atom.
I have no idea what a warm hole is, but I assume it's a whole different kettle of fish.