Are you doing two colors on the same row (like fair isle) or are you using a doubled strand of the same yarn?
For the first scenerio, make sure you always carry one yarn on the top, and the other on the bottom; if you do this with only a little slack between the knitting and the yarn ball they won't twist.
For the second senerio, the easiest way to do it is to wind them both together into one ball. You can do it with a ball winder or just follow Amy's demonstration at the bottom of this page . Thhis will require you to either cut the yarn, wind a new ball, and eave in more ends, or if you only have a few rows done it might be worth it to frog and start over.