And what's the difference between arranging the order in database and arrangingthe order via plugin?
Anyway, the key lies in the method responsible for making items to draw. It's called makeItemList and it's located in Window_SkillList in rpg_windows.js
Considering everything references the order in the database, you'd be better off just biting the bullet and reordering them. One suggestion though is to leave some gaps here and there so you have less to reorder later on (for example, I put a gap of 4 - 9 skills between skill types, in case some new skills got added late game).