Finger picking a 12-string is hard to do. The 12-string loses a lot of jangle when you use a classical free stroke (Tirando instead of Apoyando). I tried modifying the saddle so the fingers attack both strings in the course more equally. DADGADJohn also tried it a while with some success. He says it's all how you attack the strings - thumb to get the high octaves, fingers to get the lower strings. I'm trying rest strokes now and the sound is much, much better - akin to using a pick, and both strings are quite audible.
Here's a quick video:
