If anyone ever has to do this, it's actually pretty easy, at least the way I did it.
I sync my 3GS with my work laptop which has been fine all along. I updated iTunes at home last night on my personal desktop and tied it to the same iTunes account. I hooked up my old 3G and connected it. I renamed that device to 'Kids Phone' and transferred all of my apps and stuff from that phone to that iTunes library. I did the updates and then synced back to the phone without a problem.
I need to figure out how to sync podcasts and music on that phone though... because I basically just want to remove what's on it. The kids don't need my music or the few remaining podcasts on there. I think I just need to tell it that I want to sync but manage those manually. I wish there was a way to just say "I want to remove XYZ from this phone".
