I would guess that your confusion is based on the idea that DC could
be viewed as either + or - depending which way you would hook up the
leads of a DMM, or which side you determine is your reference side.
I've heard this same thing from many many technicians, "There really
isn't anything as negative voltage, it's just the way you look at it".
Well, ok in certain instances this is true. But consider this:
If you have a battery in a certain circuit and the negative side it
connected to a common earth ground and the positive side connected to
a resistor which is connected to earth ground, the electrons would
flow from ground, through the resistor, to the positive lead of the
battery. (I am horrible at drawing schematics, so I will not trouble
you with my scribbling.) Since electron current flow states that an
electron will flow to a more positive source, we can conclude that the
battery terminal was more positive than ground (0 volts). The battery
is a constant positive voltage source. Now if we had a way to cause
electrons to flow through the resistor to ground from a terminal of a
constant voltage source, ground was obviously more positive than the
terminal of the source. Guess what, you must have had a negative
voltage source. So there most definitely is such a thing as negative
voltage.
In linear devices, such as resistors, it really makes no difference
which way the current flows. But as Mr. Popelish stated, there are
devices such as op amps, discrete transistor amplifiers, etc. that
need negative voltages to function correctly.
So to sum up my ramblings, there is a difference between negative and
positive voltage sources. The positive is X volts as referenced to
ground and the negative is -X volts as referenced to ground.
I hope this helps.
Fraze