How can I separate ipad sync from iphone sync?

When I went to sync my iPhone 5 after syncing my new iPad Air for the first time, it wanted to install my iPad apps on my iPhone, even after I unchecked the box next to install new apps.
How can I ensure that my iPad syncing is completely seprate from my iPhone syncing?

The iphone is not a storage/backup device.  The sync is one way - computer to iphone.  The exception is itunes purchases:  File>Transfer Purchases
Copy everything from your other library/computer, or your backup copy, to your new library/computer

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