You just have to suck it up for a while. She'll get the message!
All hail German Shepherds! (Ok...first of all, she whines because you are her pack mate & she thinks she must protect you; no matter how small she is.) Once she gets used to sleeping with the other dogs she'll be fine. You sound like me tho...I HATE it when my puppies whine...breaks my heart!
You train dogs with daily beatings, just like children. Jk, relax! My dog has separation anxiety, and only by taking him for extended walks- 6 miles or more- have I been able to moderate this set of behaviors. Your puppy may be different. You have multiple dogs? What are the age differences?
It would be nice if one of the older dogs would bond with the puppy. I had a much older dog when I got this one, and she did not like my new friend at all. I think that's part of the reason he became so dependent on me.