How do I keep my iOS devices' apps separate?

If I have an iPhone and an iPod touch, how do I manage the apps for each device separately in iTunes?

See:
How to use multiple iPods, iPads, or iPhones with one computer
What is the best way to manage multiple...: Apple Support Communities
You can also just go to the App pane for the device in iTunes and only check the apps you want on each device.
Also, go to Settings>Store and turn off Automatic downloads

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How do I keep my iOS devices' apps separate?

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