Some stats have a white fortune die after St, To etc which I guess you add to the pool when you make a check against that characteristic. In other places such as the Basic Soldier NPC page 67 of the TofA, the fortune die is placed after the DR and Soak. When/how is this used?

I think page 67 is just a layout error. Treat it as if the fortune die were after the stat number but before the DR, Defense or Soak number that's in parenthesis.

These fortune dice all just work exactly the way PC Fortune Dice associated with Characteristics do. Any time the monster/NPC is rolling that stat, you add a white die to their pool.

Thanks Bergstrom