It subtracts negative damage from wards equivilent to the peircing you get. For example: An opponent has 20 armor peircing in all (15% from infaliable bubble, 5% from gear). You have a fortify, a tower, and 40% resist. That 20 will be reduced through the fortify, canceling it out: 20 (armor peircing)- 15(fortify)=5 left. That five that is left over in armor peircing goes to your next layer of defence, your shield: 5 (AP)- 50 (tower)= -45, so in a sense, the above senario is like your opponent only has a -45 damage shield on. If you have no shields on, then it will be like you only have 20% resist.
Now lets take the max armor peircing I can think of: 49% (Lightdancer attire: 11%+crescent ax of astrals 3%+ tc inffaliable 20%+ tc unstoppable/ extrordinary 15%), if you have a legion shield on, then the same thing will happen as teh first senario, the 49 will go throught 30, and have 19 left, and that will be subtracted from your total resist, so it seems like you only have 21 resist.