The easiest and most usual way to deal with this is:
1.) Create new vassals for the baronies (especially churches and towns, castles you could give to the count to bolster his power) via right click -> create new vassal.
2.) Pick able guys out of your court (that are of your culture and religion) and grant them the counties.
3.) Pick the guy you adore the most out of the counts and give him the ducal title.
You could also give all the counties to one duke, but be sure that he is loyal. And never make dukes that are strong enough to challenge you on their own.
Beware that sometimes the auto-generated Mayors give you wrong inheritance warnings. Be especially careful in recently conquered areas which are wrong religion. I tend to double up or even triple up on mayors and bishops. They're not gonna revolt, easier to make 5 guys happy than 15. As to Bishoprics, don't auto-create bishops. If you give a Bishopric to an existing Bishop (some Bishops, not all of them), you get +25 piety. I do not recall getting that for AI generated Bishops. One downside, Bishoprics may split up (?), but mayors tend to stay grouped forever.
As for counties, I ignore abilities or even guys I like. Only one stat matters: I want people who like me! Failing that, pick content vassals and imprison ambitious ones at the first opportunity. Keep in mind also that certain bad acts by you may not affect courtiers, but when they become Counts those negative modifiers come into play. So +40 for granting a county might be offset by other actions you've taken, actions which only pissed off the landed class. If I knew more, I'd tell you which modifiers carry over. I think some affect everyone, like Tyranny (?) while others might only affect people who were in your court when you did them. Sorry I can't be more specific, but keep that in mind.
Wrong holding penalties can be annoying, or helpful. Have an ambitious Duke who you want to revolt? If you can get him a "wrong holding" penalty at -30, that's Court Jester x3. Revolt, imprison, one free title revocation and he dies in prison. Assuming he was going to revolt anyway, of course.
Break it up. Keep your vassals weak is the name of the game. You'll be protecting them as king in any case that might arise. Once you get the Ducal title you can give it to the most loyal of those vassals and make him even more loyal while he manages the rest of those knuckleheads.
Generally speaking weak vassals rule. However, as King of Burgundy, I had one Duke in lower Italy who went nuts grabbing stuff. By the end of the game, Burgundy owned much of southern Italy, bits of Spain and a few Counties in north Germany. I hadn't lifted a finger to help (I was busy destroying France).
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