In the Bible, things that are lower down, or under, physically, generally represent things that are lower or more external spiritually. In some cases, the lower things have been separated and put away to protect the good, but in others, it can mean that a less exalted idea or good desire is supporting a more exalted one.

(References: Arcana Coelestia 4564 [1-2], 8610, 9656)

Darkness" is a state without light. "Light" is truth from the Lord, so "darkness" represents a state where truth is lacking. Here's a cogent passage from Arcana Coelestia: "The person who has yet to be regenerated is called 'a void and an empty earth', and also 'ground', in which no good or truth at all has been sown - 'void' where there is no good, and 'empty' where there is no truth. Consequently there is 'thick darkness', or stupidity and lack of knowledge about anything that has to do with faith in the Lord and so anything that has to do with spiritual and celestial life. (Arcana Coelestia 17)