The “right side” of the emboss is the “v” side of the stockinette stitches of the embossed area. You can put all of the “right sides” of the pattern on the same side of the scarf by always beginning the embossing portion of the pattern on the side of the scarf that does not show the “v” side of the stockinette stitches. If you wish to alternate the side of the scarf that the “right side” of the emboss appears on, then always begin the embossing portion of the pattern on the side of the scarf that shows the “v” side of the stockinette stitches of the preceding embossed logo section.

(Hopefully that will make sense once you’re looking at your scarf and knitting.)