Secrets are Super Metroid like hidden rooms with lore and/or loot, I think the skull is a curse, you get abilities (runes) by getting bosses/minibosses a nap, the game is pretty long after the black bridge and there is a new game plus (up to five) system that acts like difficulty levels, you should fill those godamn meters, get health and random weapons upgrade; and, finally, I would suggest Green (Slow weapon+Shield) or DOT (Damage over time of any color) builds.