Gerber Setup Options
I always check the Plot all used drill pairs for both the drill drawing and drill guide because you never know when you might need it. Regarding the advanced screen I always reference to the relative origin. The relative origin is the one you can move by going to Edit --> Origin --> Set (shortcut E-O-S). I place this origin at a large mounting hole which supposedly makes it easier for the board house to reference the other holes to it. The absolute origin, if memory serves, is the bottom left-hand corner of the PCB editor window. I don't like to use this origin because it places the actual board away from it. As for the leading and trailing zeros most board houses will not care one little bit.