No, that won't work - then your striping effect will be opposite (ask me how I know!!)
You need to start both socks at the same point in the color strip. If a 2 ft long red section leads into a 3 ft long blue section, then there's a 4 ft long red section - start both socks at the same point in the same color sequence. I've never used Circus so I'm making these colors up, but you get the idea.
Personally, I don't worry about it. I rather like any of mine that are a little bit off, just as much as the pair that goes oposite. Don't think I've ever worried about it so don't have any that match even close to perfectly. But that's just me!