That instruction is the perfect one for intarsia, but not for Fair Isle. If you're stranding the yarn, you don't want to twist it. All directions I've read and followed say to hold one 'above' and one 'below' consistently, to avoid twisting. Your main color should be on the top and the cc color on the bottom like this.
"Trust the pattern!"
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Hop aboard while we follow the cloud-covered van of knitting harmony, man!! Woooo!! --Hedgehog
IngridKH on Ravelry