Points are subtracted from the 10 points they are 'spotted' in my leagues. Actual Negative points are charged at 35 points. I like my Defense to be a factor in the outcome. Defenses can score as much as a good RB in most cases. If I don't get 20 points a game something is wrong.
I have tweaked my settings over the past years and seem to have found a happy medium.
Try this....and let the league know first... go in and change your Def settings for THIS year and see if it has the desired effects. It will change all the scores for the year and you can go back a look if your new settings do what you want them to do. And you will see what a difference in settings would have had on the outcomes. Just BE SURE to write down all your old setting and everyones totals and scores this week first so you can change them all back again. Anyway... here are my D/ST settings.
Fumble Recovery 2
Block Kick 2
Return Yards 20 yards per point
Kickoff and Punt Return Touchdowns 6