This is where the “player does not need to declare what Momentum is being used for until the time it is spent” clause comes into play. You roll your damage dice (e.g., 5 cd Piercing 1, you roll 1,3,4,4,4) and then decide what Momentum to spend on those damage dice.
You could spend 1 Momentum to reroll the 4 that were zeroes. You could spend Momentum to ignore 2 points of armor (per point) because the badguy’s out of Vigor and any damage past armor causes a Wound. You could spend Momentum to increase the damage.
You could spend Momentum to do any/all of those things. Example:
Byris the Hyrkanian hits an unhurt brigand with his bow and does 5 [cd] Piercing 1 with it. He rolls 1,3,3,4,4 on his damage dice and does NOT like the outcome. He generated four Momentum on his attack roll, and spends 1 to reroll 4 of the dice. He gets 1,2,2,3,4, a respectable 5 points of damage. He is firing on brigandine-wearing brigands (2 points of armor) and since he didn’t get an Effect, his bow’s Piercing Quality doesn’t help.
Byris could reroll again, but with only 2 dice in the reroll, he’s still unlikely to get that Piercing, and VERY unlikely to get Piercing 2. He decides to spend 1 Momentum to ignore 2 points of armor, doing [effectively] 5 points Piercing 2. This is enough to cause a Wound, but the brigand is Toughened, so he doesn’t die. Byris puts the 2 remaining Momentum into damage, doing 7 points of Vigor (and that Wound for doing 5 points or more).
Note that Byris could have spent that last two points of Momentum to fire a second shot at +1 Difficulty, had the situation called for it.