I have the same problem. This game is too hard to play and I can't figure anything out. It's been like a year and a half now, is the game still extremely confusing to get into?
The game tells you at the beginning
how it works.
You don't get XP from killing monsters, you get it from completing quests, going hunting/adventuring with Eric and reading Krowly's books in the evening at the desk in his bedroom.
It's still incredibly grindy though, especially when it comes to the non-XP gains.
Skill gains for Alchemy, farming and cooking are one point per action, and each action takes a time slot to do, and while raising affection with NPCs is a little easier, it's still pretty grindy too.
Ultimately, playing this game involves a lot of repetitive grinding for both advancement and scenes... Unless you cheat.
There is the cheat room accessed through the basement in Krowly's house to remove the affection grinding, and either RPGMaker Edit or the online Save Editor can help with the rest.