Practice, practice, practice.
Work on the top knot when she is drained of energy, after a play session or a meal or a walk. I started working with Max after his breakfast. Later I linked topknots and grooming with his favorite activity, going for a walk. He knew he had to have his hair done before he would be able to go outside. Eventually he wanted his hair done and enjoyed the attention and comfort of having his hair out of his face.
Basic obedience training helps too. Teach your pup to sit, stay, and down. My boys also understand stay still and head up.
You can train your pup to go down and rest her chin on a pillow while you do her topknot. I talk to my boys when I groom them.
Hope this helps.