They are actually treated as different devices and you can choose which Apps and content are synced separately. I think by default they are all selected, so you may have gotten them all, but when you connect your iPad and select it in iTunes, there are tabs across the top that allow you to choose what to sync.
For example, if you select the Apps tab, you can select or unselect which Apps you want synced over, and it remembers which are not selected for each device. Note there is also a check box to
[ ] Automatically sync new apps
The same selection process appies to Music, Movies, TV Shows, Podcasts, etc.
iTunes knows which device is which by the serial number on the device and will recognize the phone separately from the iPad. As ivan54 suggested, you can choose the can't content that you want to sync to each device.
Using apps as an example .....
Connect the iPad to the PC and launch iTunes.
Click on the iPad name on the left side under devices.
Click on the Apps Tab at the top of the window on the right.
Click on all of the apps in the apps list that you want to sync.
Click on the Sync Apps Heading.
Click on Apply in the lower right corner of iTunesYou can do the same thing in each tab in iTunes ... Music, photos, books, etc....with both devices... And iTunes will remember the sync settings the next time that you sync.If there is something on the iPad that you want to remove - uncheck it in the appropriate tab of iTunes to deselect it and follow that with a sync in order to remove it.