Alrighty, alrighty! Shiho-sama has come to clear (some) of your doubts! 

Firstly, I think we'll stop calling the 'sub-tiers' that, and start calling them 'Specializations', to avoid confusion. A Specialization is a new evolution of your class, as in you started as a knight, reaching tier 3 gives you the option to become Option 1 and Option 2, both of those options specialize in different ways of fighting, one may be pure offense, while the other might be defense or one may focus on sabotaging enemies and the other on buffing allies. That's the basic of 'sub-tiers', now called Specializations! 

And Perk points are the points with which you can obtain new abilities. You get one every 100 points of mastery as well as unlocking a tier. You can also get more perk points in events and from defeating different special monsters. 

Also, some of you ain't reading the CS well enough! I said, tops for Class Mastery is 200, but since that's kinda stingy from me, I'll make the tops 300, but please, don't get further than that! 

I hope that solved some of your doubts, if you still have some, please leave a comment here or PM me. Thankies!