He doesn't have "special daggers." He uses the Flying Thunder God by teleporting to places where he has a seal marked. The daggers are marked with the seal so he can throw them and teleport to where ever they land. We've seen him put the seal on other objects, such as trees, and even on people's bodies (Tobi and Bee). We already know he has put several seals on/inside of Naruto, so it wouldn't be far fetched for him to have marked Naruto with a Flying Thunder God seal, just in case.