From my experience with LDT, I would not use pipeworks to design a storm sewer system. I would use another application to design the pipes and then use pipeworks to draft them. If you aren't doing any design and are strictly drafting, Pipeworks does not handle any shapes other than circular (no boxes, arches, ellipses, triangles, rhombeses, I'm sure you get the idea). What I do in this situation is to give the pipe in pipeworks the same diameter as the height of the box (or other conduit). Some manual drafting is necessary after the final pipes are drafted (i.e. adding the other dimensions).
Brian