A package design system creates one or more package design files by creating cut line instructions and fold line instructions for a package flat. If the system determines that the package flat should be split into two or more subparts across two or more substrates or two or more sub-regions of a single substrate, 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.