Okay, I know how to do this
Here's what you need. They can all be found on Yanfly's site here:
http://yanfly.moe/yep/
-Auto Passive States
-Equip Battle Skills
-Allowed Types (EBS Sub-Plugin)
What you do is:
-Create a new skill type called "Passives" or whatever you want them to be called.
-In the parameters for the Allowed Types sub-plugin, add the IDs for all your skill types to the "Allowed Skill Types" parameter. Each ID should be separated with a comma. This will make it so that the only skills you have to equip are your passive skills.
-In the parameters for the Equip Battle Skills plugin, set the limit you want for passives (Bravely has a cap of 5.)
-Make the state that you want the passive to apply, and then make the passive skill a la Auto Passive States (make the skill, don't have it do anything, make it so that it does not appear during battle, and add the <Passive State: x> notetag to the notebox.) Make the skill part of your new "Passives" skill set.
Unfortunately, I do not know how to make a skill take up more than one slot (as some of the Bravely passives do take two or three), but I'm sure you can balance your system toward equipping five one-point passives, rather than something along the lines of one two-point passive and one three-point passive.