The rule of thumb when knitting (or crocheting) with hand painted yarns is to alternate between skeins every two rows so that the colors are spread out evenly in the garment. The unused skein is simply put the side of the garment for two rows and then gently, pulled into place. When knitting a sweater or a hat, this technique is easily hid on the wrong side. When knitting a reversible object, like a stole, it is best to cut the yarn and rejoin it in. Any loose ends will be woven into the object upon completion.
But, cutting the yarn every 2 rows and weaving in the loose ends is tedious and obnoxious. However, going to the other extreme and not altering the skeins causes splotches of color on the garment.
So, what's a knitter to do? Bite the bullet and compromise.
I have opted to swap skeins at the end of every repeat (16 rows in my pattern). The stole is still a bit splotchy, but I'm going to thumb my nose and swear that I designed it to look like that.