We just added the score a couple days ago -- still tweaking it. The concept is pretty simple:
Say your equipped gear scored as 1000.
Then you run best-in-bags, now it scores 1100.
So the percent gain is 100/1000 = 10%, so we would show +10% DPS.
If it ever shows a negative score, that is usually because you changed your spec priority. For example if I decide to change my main spec from Protection to Retribution, and move Retribution to the top of my spec priority, then run my Protection best-in-bags again, it might gem/enchant things for Retribution instead. So my Protection score will go down (because I've decided it's not as important as Retribution now), but my Retribution score will go up.
If you are a lower-level character (below 110 and/or do not have your artifact weapon), all bets are off... the scoring won't really mean that much. We'll probably add code to hide it until you get max level and an artifact.
As for changing settings -- the first time you visited the site, it should have shown a help overlay describing the stuff on the UI. You can always view it again by scrolling to the very top of the web page, then pressing the blue "Help" button in the upper-left. If you do so, it tells you that the filter/funnel icon in the top-middle of the screen has all the settings. Go in there, and you can set gem/enchant option to "None".