Subplots and organization

I'm going to admit that I haven't spent a lot of time on the novel lately, but I am anxious about getting back to it, as I am constantly thinking up ideas.

One thing I've realized is that there HAS to be a series of subplots -- something that is making the job of writing a little harder because I've realized that you can't just concentrate on the main storyline. Basically, there just wouldn't be the depth that I believe a novel requires.

My novel -- right now titled "The Father's Forgiveness" -- deals with several mainstream issues, including the death penalty (I'm intrigued right now with the Supreme Court's decision to hear a case about a guy who is scheduled to die for raping a child), as well as several religious issues which pit Catholic views against other ideologies. I grew up Catholic, and while I still hold dear to many of the Church's teachings, my thoughts on various issues (including the death penalty) differ greatly. Since one of the main characters is a priest, this is making for some great discussion in the book and has prompted a lot of soul searching on my part.

Anyway -- getting back to subplots and organization. I am considering using a tool that I learned about in a screenwriting course. I think I'm going to use 3x5 index cards to write out scenes, and then I will use those cards as puzzle pieces to create the best possible story I can imagine.

Have any of you used this technique in your writing? (I don't get a lot of comments here, but I like to pose questions in case someone stumbles upon this blog and decides to contribute.)