I'm doing a two colored scarf myself right now. What I do is, when you get to where you start with the second color, just start knitting with the second color. Leave a tail that's a few inches long. I also just leave the first color yarn on there. When I get done with the second color section, I cut the first color yarn so there's a good few inches for a tail. Then I take my yarn needle and weave in the ends, when to me is just like sewing it in. Also, when you're changing colors, make sure you change on the same side. Hope this helps.