Yes, as with all the feats you actually have to choose a die (it took me a while to work this out!). Choose the one you want to re-roll and that is the one that counts towards your weapon.
Choose the die you want to reroll. Should be outlined in Green. Then choose the method of payment. 2 Health, 1 Weapon or Armory charge (You get either 1,2 or 3 Armory charges depending on the initial skill check black die roll)