Follow the link below. It's an excellent article written by Trace Trimble. He frequents these forums. Take a look at schematic C that's the one I used. The only thing I changed when I installed my system is that I added another pump.
What I mean by parallel is that both pumps get water from the same source and both pumps pump water into the same manifold. The water manifold is responsible for diverting the water to each bag. One switch controls both pumps as if they were one. Take the time to read the article, if you haven't already. It was extremely helpful to me.
Here's the link: http://www.wakeworld.com/Articles/2001/BallastSystem1.asp