Hi Kevin,
In quiescence, during your first 3 spectra, SS Cyg has a relatively stable accretion disc which is being fed from the secondary star and is in turn transferring this hydrogen-rich material onto the surface of the white dwarf. This process produces the Balmer emission lines you see in the quiescent spectrum. When the star goes into outburst, the temperature of the disc increases elevating the blue end of the continuum, singly ionised helium HeII lines appear, and the opacity of the disc increases which absorbs some of the emerging light generating the absorption component of the spectral lines and reducing their emission component. This is a rather simplified description but conveys the general picture.
If you want to see how you can accurately flux calibrate your spectra using a V magnitude, have a look at my workshop slides in the spectroscopy section of the E&T website.
David