Malcontent - The Puzzle Box Trilogy, #2

Six months after the events of MALEVOLENT, Mal and Libby are struggling with the side effects of having two souls combined in one body...and the uncomfortable intimacy it brings. When Mal captures a hive of killer bees, they inform him of a new threat from the Necromancer. Dark barriers and dangerous sigils are mounted around the valley. At the same time, Libby begins training with the Marchers, who will instruct her in the use of life and death motes.
But the Marchers are on a relentless hunt for the Lich Prince and his hidden soul - which she now carries inside of her. Now Mal and Libby must find a way to extract Mal's soul before they are caught by the Marchers - killed by the Necromancer - or destroyed by the slow subsumption of their souls.