First you roll to hit with a d20.
Then you roll the damage with the relevant number of other dice (d10, 2d6, etc.).
Then you roll to see what % of the blade actually penetrates, using d%.
Then you modify the damage by the percentage of blade penetration.
Then you multiply damage by the weapon's sharpness (usually a multiple of .25).
And when you're actually doing damage, you:
Subtract armor from the damage done.
Roll d% to determine where the weapon hits, in general (like, right arm).
Roll 2d6 to determine where the weapon hits, specifically (like, front of forearm).
Count the points of damage against the thickness of the hit location, rolling randomly where indicated for arterial, organ, or bone damage, and counting bones as armor where need be.
I seem to remember most ballistic attacks having a chance of hydrostatic shock, and almost all attacks having a small chance of causing immediate death shock.