(Not) synchronizing apps across multiple devices; how to?

Sorry if this sounds like a dumb question, but I would like to sync an iPhone and iPod touch with iTunes but do not want the same apps and content on both devices. I know I can set what to sync individually when it comes to movies, music and photos.
When I transferred my apps from iPod to iPhone (the iPod prior to this did not sync apps), all I did was press sync, then connected the iPhone and pressed sync and all (well, almost. 12 went missing, including two paid ones) went over. So it seems that whatever apps synchronized to iTunes will sync across all devices connected to it.
Which is good when I want to transfer but I don't want it now. I try to stop app sync between iPod and iTunes and it tells me "all existing applications and data will be erased". How do I manage apps on each device individually?
Cheerio,
Nicholas.

Sign into iCloud with the same Apple ID on all your devices:
Settings > iCloud

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