The "dots" on the gears are really the ends of the bolts that hold the big gear to the shaft. There should be a small punch mark on the big gear. There should also be a small punch mark on the small gear. They gears should be set up so that they are adjacent to each other when the engine is assembled. This should put the piston at Top Dead Center.

If you cannot see the small punch marks, you may have to do some cleaning of the gears, because there should be the marks.