Oh.... I think you're saying that the yarn isn't just varigated but changes color from light to dark blue and back again and you're asking if you should match the hues of the two yarns or "random" as in one yarn might be going to the lighter blue before the other?
Even if that's not what you're asking, (lol) you can do up a little swatch containing the styles you're trying to decide between to help you.
I'll bet it would look fine either way and sound like it would much less troublesome to do it "randomly" or start with the colors close and if they get "off so what. I've never knitted 2 strands of varigated yarn sideways before so take it for what it's worth.