It sounds more like a case of separation anxiety. Have you tried searching the forum for that topic? There are tons of threads on it and some very good advice. If it is separation anxiety you can nip that in the bud but you have to get on it immediately. Good luck!
I'd be VERY surprised if it's separation anxiety with this puppy... I know her big brother quite well,
and he drove me to distraction with demand barking from 8-18 months.
Unfortunately, there are no quick fixes for demand barking, but if you are consistent, it DOES get better as they mature. I was ready to tear my hair out in the middle of it, but now it has faded into a (semi) amusing dream!
We tried, as much as possible, just to ignore demand barking (easier said than done!) If that wasn't possible and he wouldn't stop, he was put gently in his crate, where he stayed until he was quiet. He even barked at me in classes, when it wasn't our turn... he had to be DOING something ALWAYS!!! I can't tell you how many times I marched him out of the ring to show him that he didn't get what he wanted (me working with him) by barking at me.
Suzi is correct that at least from your description, it doesn't sound like you are using the clicker correctly, and it could actually be adding to the problem. A clicker is a better tool for teaching an animal to DO something than it is for extinguishing an unwanted behavior anyway. You might want to work with a trainer a bit to help you set things up as much as possible for success, and to teach you strategies for handling her demand barking when it occurs.