I think your question is how to make by jig work for box joints. Sometimes the correct answer to to toss it and get something else. These type dovetail jigs do a good job of dovetails but are lousy at anything else. I have an I-Box from Incra and it makes flawless box joints. I also have a 25" Incra positioner that can make them but the I-Box is so simple and elegant. You have an initial adjustment but after it is set up you just put it on the table saw, adjust the blade height and bam you are making box joints. There are many ways to skin a cat and in the end you have a skined cat. But usually the real question is what is the most efficient way to skin a cat. In the case of box joints your skinned cat is the I-Box.
If you really want the PC jig to work then cut some plywood the same width as your project, mark your inner and outer sides and number the sides to see how to get your grain match the way you want it. When you perfect the operation with the plywood you will be a master of the jig and can make it on your good project work. There is no better teacher than repetition.