Are you using the skill tree in the main menu? It should make the fights a lot easier.
I have, but I'm still doing basically zero damage to mobs in the 4th dungeon regardless of what I'm using and even with some HP buffs and defense buffs from the tree I still can't survive more than two rounds of hits in the dungeon. Now I don't know if it's some weirdness from a legacy save but I only had 11 points and there are...a lot of skill trees.
Like I said I like the game, probably one of the best RPG maker games I've played, but this is really souring the experience.