Select the Specify Edge tool (scissors icon). Click on edges you want to be cut (open seams). Hold Ctrl to select multiple. For the edges you want to remain connected (folds), leave them unselected. The goal is to cut the model into 2D islands that are small enough to fit on paper but large enough to minimize gluing.
You can adjust the width, angle, and shape of glue tabs. New in 6.0.3 is the "Reinforcement Flap" option, which automatically generates internal support tabs for large, flat surfaces that would otherwise warp. Pepakura Designer 6.0.3