At the moment the layouts are created with a "good enough" solution.
This problem is known as The Knapsack Problem. It is an "NP-hard" problem, which means "there is no known polynomial algorithm which can tell, given a solution, whether it is optimal".
The current implementation is an approximation of getting all the pieces on the paper size selected. It is not focused on optimization of paper usage. We have plans to incorporate a solution in the future, one that has an option to take the grainline as input into the placement, and optimizes paper/fabric usage.
For now, if you would like to manually improve the layout, you should create the layout for the paper size you need. Then select File/Layout/Export As, and select SVG. Open this SVG file in Inkscape or Adobe Illustrator and improve the arrangement.