If i have a signal at 1 Hz, and on the oscilloscope I displayed the FFT (fourier tranform) what does each RED line mean? I understand the fundamental freqency so there is a harmonic at each multiple, but what do the magnitudes represent?
you have a non sinusoidal continuous wave input thus what you get in your spectrum is not only harmonics, its other frequency components found in the signal and with its megnitude on y axis.
fourier transform represents a continuos wave form as an addition of many sine waves with different megnitudes. you will get frequency on x axis and megnitude / power on y axis depends on the setting.
As long as a plot for FFT is calculated with fewer than an infinite number of perfect samples, it will contain artifacts from the process.
Your oscilloscope has offered some hints. "Low signal amplitude" means that the instrument is not receiving enough signal to even make the best of its meager accuracy. "Unstable histogram" is the scope telling you that it doesn't believe its own calculations.