If your characters' base classes are set by default from the beginning, I would tie the prestige (or "secondary" in your case) classes to class quests. When the quest is completed, that particular class would be unlocked for the party and any character, who had already mastered the base class, would be able to switch to (or equip if you are going the secondary class way) that class.
For example: Eric is a warrior and when he reaches level 10 and learns every warrior skill (unless they are earned automatically at certain levels), he can take on a quest to learn the way of gladiators. Let's say, he goes to the arena, speaks to whoever in charge, that guy tells Eric that he has to prove himself first in the arena. Eric goes into a series of fights then maybe some other quests like "speak to X, learn some tips and tricks from them then i will let you fight Y (so you can progress further in the arena)" and when he finally is the ultimate winner of the arena, the quest starter guy unlocks the class for him. You can even add aditional side quests related to his fame in the arena and in the end he can even learn a special gladiator skill or something.
If your characters' base classes are planned to be changable on the go like Final Fantasy Tactics games, I would go with a class tree system (again like FFT games) or something similar. Also, you do NOT have to have every higher tier class require more than one base class. You can just make it like; warrior level 5 -> monk is unlocked. Problem is, if you take this approach, you will most likely need to turn some of your secondary classes into tertiary or even quaternary classes or create more base classes to match your secondary classes. If you don't want a class tree system or some sort of class related side quests to add flavor to your class system, then you can just make it so that when a character's base class reaches a certain treshold, all the secondary classes attached to that base will be unlocked for that character.
For example; You want Eric to be a Dark Knight. You reach level 5 Warrior and level 5 Black Mage on Eric and as a result you unlock Dark Knight for the whole party as long as they meet the requirements.
However, this system may end up hard to implement depending whether it is easy to relate certain base and higher rank classes to each other or not. It isn't hard to say; "Ok, you already have warrior and black mage as base classes and dark knight as a secondary class so why not just tie those two to dark knight, it makes sense!" but for some classes in your mind, it may not be as easy so you might need to reconsider your class list.
I hope I was of any help

Good luck with your project.
Edit: Check this out:
http://finalfantasy.wikia.com/wiki/List_of_Final_Fantasy_Tactics_Jobs It will give you an idea about branching out your jobs.