Hi Andy,
At it's most basic explanation:
No matter which colour of line you are adjusting, the others will move to some degree also. The Yellow is the Peak energy content of the track you have loaded and the green is the average.
So, for example, if you adjust the Yellow line at a particular frequency then the green must also move because when you adjust the Yellow you are changing the value (energy value at that frequency) of the peak and if you change the value of a peak of something then that also alters what the avarage is, hence the Green has to change also.
My advice would be to find a piece of music that is not recorded very well (like a bootleg recording for example) and load it into Harbal and see how bad the Spectrum looks. Just dive in and start to adjust the spectrum (with the EQ button on) until it looks radically better/ smoother. Then sit back and switch the EQ button on and off to hear the difference.
You may have made it worse (but with most bootlegs I've heard, that's unlikely) but at least you have made a Harbal start.
Keep at it, it will make sense I promise...
