Just knit with the yarn you've been using for 41 stitches. Drop that strand, and start knitting with a new ball for the rest of the row.
Check the next line in the directions. I bet they say something to the effect that you're to purl back 41, put X amount of stitches on a holder, and then, with the other strand you left behind, you'll purl to the end of that side.
Now you have your two shoulders on the needles, each with their own strand of yarn, since they're no longer connected.