There are only two levels of CH as far as I know. Getting CH on multihit moves add up the CH stun time.
In CC, The stun system feels like everything is a CH2 (long counterhit stun on special moves) to replace the level-1 'armor' system from vanilla MBAA to PS2 MBAA.
Combo system in general MB is quite intuitive. You can pretty much cancel anything into everything, that is, cancel from normals to any other 'level' normal which is termed reverse beat in MB. This is useful for some character's BnB, random hitconfirms, and especially useful in recovering from blockstrings. The idea is that you cancel your heavy attack into a light attack to shorten the recoveries. You'll be left with less disadvantage, but if you mix up where and when you put in reverse beats (most characters in MB have looong cancel windows on their normals) and specials, they'll have to think twice in poking/jumping out of blockstrings. Think of it like BB Tsubaki's drive canceling.
MB's air game gives out the highest risk and reward. You land a CH in the air, the opponent cannot tech until they touch the ground and you can do anything to them during that state. In a reverse situation, you'll be eating a big combo.