You have the right idea on hooking them up, but you can't just plug both batteries' balance connectors into the balancer at the same time. I just came up with a (simple) way to be able to balance two packs as one. Here's a picture of my version:
The only downside is that I can't balance the packs separately, but that's not a problem for me (they'll always be charged together). If you want me to draw up a detailed explanation of the wiring I can, but basically you can see that the power wires for the separate packs are connected in series using the series adapter, and the two wires can be disconnected from the balance connector so that the packs can be split apart in an application where they can't be so close together.