I think the yarn is suited best for top down, one piece or in the round items for that reason. I am working on a top down raglan and it is working nicely. I am going to do the dress next and had already planned to do the body in one piece.
I don't think there is anyway to avoid that when the item is knit in pieces and seamed. Even if you make note of where on the yarn you started it isn't going to match up because for the back pieces will be a different width than the front so while the back pieces will match up the front and back seams will not. Although the back pieces matching will look better than not.
So, if you were making two identicl back pieces you would start each piece at the same place in the yarn. I think that because the yarn is machine dyed not hand dyed you should have the same amount of yarn in each pattern. So for example, I am currently knitting with "Easter Basket", if I wanted my pieces to match I would chose one of the colors, purple for example, and make sure that I started each piece at the same place in purple.
Does that make sense?