Fourier Transform negative amplitude meaning
The fft returns complex values, to get the amplitude you need to take the abs( ). The real and imaginary portion tell you about the signals phase. Remember the fft is changing the basis by projecting your signal onto a complex sinusoid:
$$e^{i \omega t} = \cos(\omega t) + i \sin(\omega t)$$

and thus your signal is now a set of complex sinusoids which have some phase and amplitude. Think about the phase of a vector $v = [a, \, i\cdot b]$ on the complex plane and what this would mean.