I actually like the double run look since I can see the design a little better....but if I wanted only a single run, I would just watch the design as it stitched out and slow the speed as it approached the end of 1st run, and Stop button when it was done.
You mentioned using the embroidery designs on a quilting machine....I have the Janome 12000 which is sewing/embroidery, what machine are you using? is there a special "quilting" machine (other than a long-arm system) which uses embroidery designs?