Put them both on the same account on the same computer.You will be able to select which apps sync with which device in iTunes.
You'll also be able to pick and choose what songs, play lists, artists, etc sync with each device. I do this now, though it did take a little sorting out on the iPod Touch. I had never turned off auto-sync, so the first time I hooked it up, after a long time not using it, it ended up with every compatible app on it.
So, to keep the syncing under control, first go into iTunes Preferences, the device tab, and choose not to auto-sync your devices.
That way you can set the sync preferences the way you want them first, and then manualy sync.
In short, not a problem