Naked Necks can be very difficult to integrate. My best success story is to raise them with a different, bossier breed from chicks. I raised mine with Barred Rocks and an Ameracauna, and because they had to learn to stick up for themselves as babies, they developed into tougher birds. My two Turkins are now the top of the pecking order.
I think you're doing the right thing by separating them. Winter seems to be harder on them then other, fully-feathered birds. If you have the space, I think that it probably would be beneficial to put a dog-kennel run (a kennel with a wire pen around it) inside your other run, if that's possible, to help them integrate better in to the flock, and then let them run with the rest when it becomes colder. If you must separate them for longer then that, I would recommend putting a heat lamp in there with them, if you haven't already.
I know that this can be difficult and complicated, but it's worth it! Naked Necks, or Turkins, are a relatively weak breed, but are amazing!
Keep an eye on them (especially the vent the neck); they are very vulnerable to attacks from other chickens.
I hope this helps! If you need any more help, I would be happy to give it!
