When the raid is over, and all adjustments have been looked over and verified, press the enter button to have your DKP Scribe do the math.
When the enter button is pushed, the new DKP totals will show up to the right of the old totals.
As of version 2.0 new totals can go negative if the "Allow negative" check box is checked in the settings screen. Otherwise a negative number will convert to 0.