Hi Stacey
As you say in your case it's character that determines leadership, where as in the wild a physically impaired dog would be attacked and threatened until it became submissive and allowed it's opponent to become leader.
We have domesticated these animals and so we have already confused the natural way in which a pack works.Because of this we have to become the Alpha, if we allow our domesticated animals to completely live as a pack would in the wild we would be in serious trouble, and your top female would probably be chastised by the bottom of your pack at the moment for leadership..IMHO

I have 7 Gsd's and a x patterdale at the moment....3 adult males, 3 adult females ,and a 6 month female puppy...and the x patterdale who is also an adult male.
My top female went to doggy heaven in the latter part of last year, bless her.
She was quite small,excellent temperament, bomb proof and happy to get on with any other male/female but if they over stepped the mark she would open her mouth and give a deep growl..no barring of the teeth...but it worked ..and the one that was in trouble would then creep around her and lick her mouth.
I left her to get on with that, but if I thought she was getting to big for her boots, I would reprimand her with words in a deep voice..she knew then to behave.She would guard her food until the others had eaten and eat last..with her puppies she was just plain amazing, loved them to bits, allowed the other dogs to interact them and would even allow one of my Males ( Bombom ) to lay with the pups in the whelping box..when they were about two weeks old, she even fostered two pups within her own litter with no problem.So really she was top dog with a head on her shoulders I spose and understood diplomacy.
She was an absolute treasure, she kept them all in their place but was also gentle and trusting.
The two eldest Males however can't get along, they would fight...so I don't leave them to it, they are kept apart, but each of them will interact with all the others with no problems at all.
The others have their pecking order but there's not alot between them really, different characters but none aggressive, but they all know who's the big boss ha ha.

Tracey