What is the meaning of negative value of alternating waves?
It is used to indicate a phase relationship.  A negative amplitude on an AC value indicates that it is 180 degrees out of phase with whatever convention we have picked for positive values.

To explain better, let's look at the simple circuit below.

The relationship here is:

\$v(t) = i(t) \cdot R\$

Note that to be careful, you have to use time dependent voltage and current values.
Assuming that v(t) is a negative amplitude AC sine wave, you will get something like this.

\$-A_Vsin(\omega t) = i(t) \cdot R\$

But from trigonometry, this is equivalent to this, which is just 180 degrees out of phase with the equivalent positive amplitude sine wave.

\$A_Vsin(-\omega t) = i(t) \cdot R\$

So, physically, a negative amplitude AC wave is just another way of describing a 180 degree phase shifted AC wave.



Note also what the sign used on the schematic actually means for AC.  In the schematic, current is marked as going clockwise.  This does not mean that the current is always flowing in that direction.  Let's say we evaluate \$i(t)\$ at a particular time and get a positive result.  This arrow just says that positive results mean clockwise current flow.  If we get a negative result at a particular time, then current is flowing opposite the arrow, or counter-clockwise.