Lyric discussion by LesBovineEyes 

//Leave it on the hottest day To sink this quarry under//

To sink a quarry means to take down a victim from what it seems in this context.

//What the murder on the pride would bring Lion, crow, your kingdom Loaded in the stone heart I couldn't keep the woods in you//

The man she loves has a cold heart, someone who she knows is murderous in an emotional sense, and will probably some how victimize her heart. He has the "woods in him" or he is dangerous for her. The "pride" here could be symbolic of the girl, the man's family, whatever else that belongs to the man; he is committing some sort of an act that is harming the "pride".

//You had to learn about the hardest things The softest side would leave you//

//And on days like these I could take apart my window So let down I was so let down//

(chorus): //How deep is this soul I feel I'm in? Seen a lot of light and done a lot with it How deep is this hole I feel I'm in? Seen a lot of light and done a lot with it//

She is into him still, he still feels his soul and wonder how far in she is in to retract her heart out of the "woods".

... Just my interpretation of the first part, don't know about the rest!

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