Hilbert2 beat me to it, but here is my reply anyway.
The zero of energy is purely arbitrary. For example, you can put the zero of potential gravitational energy at the surface of the Earth, at the center of the Earth, or on the Moon. The same object in the same state can thus have positive, negative, or zero potential energy.
The sign of a change in potential energy tells you something about what happend. If the sign is positive, then energy was put into the system to bring it to its current state. If it is negative, energy was taken out. Using again the example of gravity, if I lift an object from the floor, it gains potential energy (positive sign for the change). If I let it drop, it will lose potential energy (negative sign for the change) as it gets converted to kinetic energy.