The clues for Samara's Large Secret are the clues you need to free Primrose from prison. Look at the Alley for clues after you talk to Primrose and she tells you what happened in the night Merek died. After that, go talk to the Crone and you'll find one more clue, but I don't think this one is that important now.
For Primrose, you need to find out about the Library's financial problem. I think you do that by working there. Then find out about the kind of books Primrose borrowed, then what Primrose "did to Merek". Well, the last one you discover after talking to Samara.
After you confront Primrose, you can go to Samara and do the same.
I may be off in a few things, 'cause I didn't save before confronting her, so I couldn't do the process again to tell you exactly what to do, but without spoiling the plot, this is basically what you need to do.