The panel on the right-hand side without light is covering an Energy Vial; use it later if you're running low on health. Now take the middle path through more spiked glass and use the Earth Rune at ...

This first area is very simple. All you need to do is push the big wooden crates into the doorways. This will allow you to use the crates as steps. As you progress, the ship will start rocking, making ...