If it's weaving, each color is on a separate shuttle, so I don't see where it would be a problem.
But if you're talking about knitting, it would be a big problem, so I'm guessing that's what it is.
If you're knitting fair isle, with a lot of small patches of color, Euny Jang recommended on Knitting Daily to cut strands of yarn about 2 or 3 yards long and just knit with them. They tangle, but you just pull on the end nearest the needles, and the strand slides right out of the mess. I've tried it and it works well.
If you're using two colors, I'd put each ball in a bowl, with one bowl on either side of me.
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