Once you've successfully changed colors, keep knitting in the new color until you want to change colors again. You can add a third color or go back to the first, whichever you like.
The method is the same regardless of how many colors you use.
If you want to add a little extra stability to the joins while you're knitting, you can tie the yarn tails of the two different colors together, just make sure you untie them before you weave in the ends.
If you're planning to change back to the original color and your stripes are only a couple of inches wide or narrower, you can also weave the old color yarn up the side of the work by wrapping the working yarn around that yarn each time you get back to that yarn ball. Then when you switch colors the yarn is right where you need it to be and you don't have to weave in so many ends.