If you just knit with the second colour you don't have anything to worry about it being the wrong colour. Just make sure your working yarn is the colour you want to be knitting. So if you have been knitting with red and now want a white stripe, make sure the yarn you are holding is white, and you're good to go.
Here is an example of how stripes turn out.
The left side is the wrong side (ws) of the work, and the right picture is the right side (rs) of the work.
If you are knitting stockinette you will have both on opposite sides of the work.
If you are knitting garter stitch, your stripes will look like the first picture on both sides. There will be a noticeable join, where the two colours looped together, which is why the first picture has so many tiny stripes blended into it.
I got the pictures from http://www.houghtonavenue.com/how-to-knit-stripes.htmlI hope this is helpful, there are also videos here at knitting help under knitting tips, on how to join different colours of yarn.