I am in that same situation with a strong willed 6 month old GSD male. It requires a lot of training and management from the day you bring in your pup to keep the small dog safe and happy and you sane.
Technically the older dog should be in charge of a pup but the pup will quickly figure out that he/she is much stronger than the older one and it is an unnatural situation. Do not let that small dog "take hits" because it will get her injured or worse.
Deja, GSD, sable WL, female, born 11 / 2013
Cam, Rough Collie, sable, male, born 8/2015