Bukkit

What is the issue?
How do I allow certain ranks to be able to bypass the protections

Please provide any additional information below.

I want to know the permission node for PermissionsEx and i want the rank to be able to bypass and build in a protected area

Since ProtectionStones uses WorldGuard for all it's protection you need to use the WorldGuard Permission (which is also listed on the bottom of the Permissions Page):

worldguard.region.bypass.<world> or worldguard.region.bypass.*

And if you want to bypass /ps commands that check a region for the players ownership, just give the player the following permission:

protectionstones.superowner