Honestly, the only way to learn the game is to jump in and play. Play as a vassal Duke your first game (an HRE Duke in the 1,066 start is ideal), so that you can muck around and see what happens. Learn marriage mechanics, claiming, warring, catholic mechanics, holy warring, crusading, managing vassals, being a vassal, etc.
There's no quick "How-To" for CK2, but the best tutorial is clocking 30 hours randomly and learning by doing.
A good example is I noticed my heir was a kinsman, but I have a son. I went into the laws, and tried to nominate my son as heir, but he was only a pretender after I done this. I just have no idea wtf is going on half the time. What does it then mean if a kinsman inherits my title rather than my son. This is one tiny aspect of what I mean. Ive watched many tutorials now, but they assume a basic knowledge of this medieval set up and how things link together, which is the part im missing.
It sounds like you're on Elective Succession (Or Tanistry, which is Elective but only for your kin/dynasty). Which means not only do you have to elect your son, but you have to convince your vassals/fellow nobles to also elect him (Through managing your opinion modifiers; make them all like you and they'll vote your way).
Of course, it doesn't matter if your kin inherits instead of your son. You'll play as whoever is listed as your heir (Providing they're of the same dynasty), which is determined by your Succession type (Elective/Tanistry: Everyone gets a vote, Primogeniture: Oldest son inherits all, Ultimogeniture: Youngest son inherits all, Gavelkind: Lands [Demense] is split among all sons, Seniority: Eldest kinsman inherits all). Of course, it also takes into consideration the gender law as well (From Agnatic, only men can inherit, to Agnatic-Cognatic, women can inherit if there's no men, to Cognatic, only women can inherit [Available for Basque culture and Cathar religion]).
Then there's religion modifiers for determined which Succession law you can use. Pagans ONLY get Gavelkind, and Muslims ONLY get Open (Strongest son inherits [Land your favourite, ignore the rest]).
Like I said. Muck around. The best learning process is to actively try and do things wrong and see how long it takes to get a gameover.