Add a second row to the scorecard and mark it "Stableford - Gross." Then add a third row marked "Stableford - Net." After each hole, calculate your Stableford points based on your gross and net strokes, respectively, and place your points in the appropriate box. At the end of each nine, add up your net Stableford points, then combine at the end of the round for your net Stableford score.
You can, if you'd prefer, use just two rows - a top row for strokes, and a second row for Stableford net and gross. In this case, on the Stableford row use slashes to divide the boxes on holes where you'll be taking strokes (same as you would for stroke play, as in the top row above).