I don't think the Yahoo autodraft free leagues allow you to specify that only 2 catchers be drafted, for example. That's the chance you take when you autodraft.
One thing you might try - move all catchers except the top 10 or so off your pre-set rankings. I'm guessing that you can rank your top 252 players (12 teams x 21 rounds), so move guys like B. Molina, LoDuca, and Estrada out of your Top 252.
All that being said, I'm thinking that you getting 3 catchers last year was a bit unusual, and might not happen again this time. Good luck!