Spectrum Window
The spectrum window shows all displayed spectra. The Current column of buttons ("C") allows one to alter the current spectra. Extracted spectra will be added to this slot. When altering the display properties of the spectra, this spectrum will the the one that is affected. The Plot column of buttons ("P") allows one to change which loaded spectra are plotted. When the Show button is clicked, a new display of spectrum properties is displayed. This button then changes to Hide to hide these properties.
Plot Window
The plot window shows the results of the interactive plots, as well as the histograms of the region pixel values. As I don't find this very useful, I haven't put much work into it.