My morality went to 20 after I picked the canibalism trait, since then I've tried doing quest to raise it back as NPC patrols are annoying but it keeps going down, every now and then. I only did Cecily 1st rescue quest and my moral went from 23.7 to 22.7. Any help how to deal with this? Thanks.

this sounds like something from a mod anyways the best way to get back morality is to donate to the church as long as you don't have under a certain amount they should let you donate

I also recommend using the church to raise morality. Personally, I've never encountered a situation where it was excessively low apart from that one quest. 

Though, eating Human flesh lowers morality, so maybe you're getting too hungies. Try to eat normal stuff, and if all else fails, monitor it closely and diagnose when it drops.

the human flesh only reduces morality by 0.1 so you would have to really go at it to end up with lethally low morality unless you are currently a moot