The characters can be integrated by having them meet in a crossover world. For example, Naruto characters could be transported to the Claymore world and vice versa. They could then exchange their fighting techniques. Naruto characters could teach the Claymores about chakra control, while Claymores could show Naruto characters how to use their yoki - enhanced weapons.
The Naruto characters are used to a world of ninjastic and chakra - based powers. When they meet the Claymore characters, who have a different set of powers based on their yoma - human nature, there would be initial confusion. For example, Naruto might be very curious about the Claymore swords and how they are used. The Claymore characters, like Clare, would be cautious about Naruto's exuberant personality and his powerful chakra. But eventually, they could learn from each other. Naruto could teach them about teamwork in a different way than they are used to in the Claymore world, and the Claymores could show Naruto how to be more stealthy and precise like they are when hunting yoma.