Hi S. --
Oh have I been there. DS didn't sleep through the night till he was over 4. Big part was my fault. Every time he made a peep I was in there to check on him.
I now know that babies need a few minutes to learn to put themselves back to sleep (I did much better with DD as I couldn't run in every time she cried, like if I was busy with her older brother)... but having another child in the same room really makes that impossible. And unfortunately your little one knows that if she fusses you'll come in.
If you can't separate the kids, you may want to try eliminating her afternoon nap (I know I neede that afternoon break!) as that may make her tired enough to sleep through the night.
Good luck. I know this was so hard on us.
S.