I had an '03, and I don't think much changed between the years. You will want to put both sacs on the same side of the boat, maybe both in the storage compartment, or one in and the other on the seats.
I used to surf with the factory ballast, and a 500# sac on the seats on the side I wanted to surf. Made a pretty good wave
Just remember to put someone up in the bow too, you still need some weight up front to clean up the wave.
2006 X-2, MCX, Slate Grey w/ Pro Tour Red accents