I think you might be over thinking the whole short row process as it is really very simple. Have you started working on the pattern yet? If you do exactly as it says it will start out looking all wonky but as you progress the shaping will start to make sense. In the beginning, it will look as if you are doing something wrong, but keep going and soon your pattern will begin to take shape.
Short row knitting is simply knitting over a portion of stitches in a row and leaving a certain amount of stitches live on the needle. You work the required number of stitches and turn your piece before you have knit the rest of the stitches on the needle. Then you work your piece back to the beginning. Eventually you will reach a row in your piece that requires you to knit across all the stitches on your needle and then begin the process of short rows again to make the next part of the scarf.
I think the video on this site is one of the clearest explanations of what a short row is and how to work it. There is also a good explanation of it in this article
Really, my best advice is to trust the pattern ( I'm stealing that from Ingrid
) Follow the directions and see how it comes out.