This is a big pain every year, and even this year with that big breakthrough feature, Konami have screwed it up on some teams - eg AS Roma have the home kit of red shirt white shorts and black socks, then the all white away kit. So you can't create the white shirt-black shorts that you need when they play away at certain other teams. Whereas if they'd given black shorts to Roma away, you could still have chosen the all white kit by using home shorts.
I remember on my last patch cut-and-pasting some teams home shorts and away shorts and swapping them, just so that their away kit didn't clash. At least we won't have to do that this time, assuming the kit insertion is ever fixed.