There are different techniques you can use when plying colored yarns, and they will give you different results.
I will sometimes ply the regular way in which the two singles are twisted around each other. On yarns with varying colors, such as those made with hand-painted rovings, this will result in a candy cane stripe effect.
Most of the time when I'm plying these hand painted yarns, I'll use the Navajo plying method. This makes a triple-plied yarn in which the colors match up with very little striping.
In the picture the Navajo- plied yarn is on the left and the regular two-ply is on the right. These were spun from the same hand-painted roving.