As soon as the puppy reaches the age of three months, it should be placed with the flock. What this is doing is letting the natural guarding instinct of the dog know this is his flock to take care of and protect. Now when you do this, you do have to keep an eye on the puppy, since he is likely to try to play with his flock. He will out grow this in a few months, but if the puppy over does it, the flock can actually become overworked and die. Minimum play is the best for the dog to bond with their flock. This is how they become the protector.
As you know, bonding is how the Anatolian Shepherd learns what to protect. Therefore, some play is required to form an unbreakable bond. The unfortunate problem with bonding is that if they bond with sheep, later in life it may be hard to have them bond with other livestock. They will be faithful to their flock and may not protect other livestock as well.
Living with the Flock
The puppy should remain with the flock at all times. There is no room for deviation when training the puppy to stay and guard their flock. If you place the puppy in the cage with the flock for a few hours and then allow them to leave for the rest of the day, they will not learn what they are supposed to do.
The Anatolian puppy should remain with the flock and have access to food and water as well as shelter from the elements. This need will change, as they grow older. If the puppy is too playful with their new flock, you could confine him with wire fencing until he grows out of the playful stage, although they do need some bonding play.
Introducing the Walk
If you have a puppy, you need to have them on a leash when taking the flock to pasture. This is how they will learn where their flock is going and they can then stand guard. You should start the walk out to a short distance since you do not want to overexert the puppy or make his pads sore from the rugged terrain. Short distances with a little longer distance added every few days would help the puppy build up strength and tolerance. This is an important step in training. If the puppy needs to return to the stable, you need to take a few of their flock along. They need to learn that they have to take the flock whenever they go out or come home.
If you take the steps to bond the puppy with the flock, they will become the best guardian of this particular livestock. It is possible to have sheep and goats together in pasture as long as the dog was raised with both. If they were raised with one only, they will protect that one. You should also start the puppy out with baby livestock as well. They could easily be injured if the adults kick at them in anger or intrusion.