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Then how do I keep it from sending all my iPhone apps to the iPad?

In iTunes, with your iPad plugged into your computer set syncing to manual and to only sync checked items. Then click on the apps tab at the top and uncheck the apps you do not want installed. Unfortunately its a messy process that Apple made unnecessarily difficult. Hopefully it will clean up this GUI garbage in the next major iTunes update...or sooner.
 
In iTunes, with your iPad plugged into your computer set syncing to manual and to only sync checked items. Then click on the apps tab at the top and uncheck the apps you do not want installed. Unfortunately its a messy process that Apple made unnecessarily difficult. Hopefully it will clean up this GUI garbage in the next major iTunes update...or sooner.

The manual sync and sync only checked items settings only apply to music, video, podcasts, etc. Apps are separate from all that, and only checked apps are synced no matter how the manual sync and sync only checked items are set.

I've heard that if you control+click on any app's check box, it'll toggle the checks for all apps. That way you can uncheck all apps at once then just check the ones you want to install. Another way to do this if you have the time is to just let iTunes install all apps, then delete the ones you don't want off the iPad. Once you delete an app from the iPad, it should stay deleted next time you sync. Whichever way you do it, it's a clunky process, but you only have to do it the first time you sync.
 
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