A package design system creates one or more package design files by creating cut line instructions and fold line instructions. If the system determines that the package should be split across two or more substrates, it will select a fold line and convert the selected fold line to a seam. Conversion to a seam may occur by creating cut line instructions for the selected fold line, imparting a first set of functional elements on a first side of the seam, and imparting a second set of functional elements on a second side of the seam. The first set of functional elements and the second set of functional elements will form a functional connection when the three-dimensional structure is formed.