Variegated floss is used to create interesting effects and one-of-a-kind pictures. While you are always free to do as the spirit moves you, there are some more organized approaches. The following is one method, but is by no means the only one. Read DMC's pamphlet #15235 "Cross Stitch with Variegated Floss" for information on another.
Remove the floss from the skein and wind it lengthwise around a yardstick. Those of you living in countries on the metric system might have to saw a few centimeters off the end of a meter stick. Carefully cut the floss at the middle and at each end, to give you four groups of floss. Two groups should be lighter and two should be darker, overall. Combine the two lighter groups together and consider them to be one group. Do the same with the two darker groups. As you stitch the design, complete each X as you go.