Are you knitting flat or in the round? If you are knitting flat, you may be able to avoid the twist problem by paying attention to which way you turn the work when you switch your needles from one hand to the other.
Start by untwisting your yarns so that they are once again 2 separate strands coming from their individual skeins. Knit a row, then switch the needle to your other hand as you normally would. Before you start knitting the next row, look at your strands. They are now crossed. Knit the next row. Before switching the needle to your other hand, look carefully at the way your strands are crossed and, while switching the needle to your other hand, turn the work in the opposite direction so that the strands are no longer crossed.
As long as you turn your skeins stay lined up (I think this is easier with center pull balls since the skeins don't bounce about like they do when you knit from the outside) and you turn your work in alternating directions when switching the needle to your other hand, you can avoid the twisting problem! I was so excited when I figured this out recently.

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