Syncing Ipad & iPhone in Seperate Folders

Need some advice. I currently have an iPad and will be getting the iPhone 4s soon. I want to keep the apps, music, photo's and video's in seperate folders, so when I sync or backup a device it would save it in designated folder. Would you suggest making 2 seperate folder's 1 for the iPad & 1 for iPhone, I don't want the same apps, etc.,  on each device or visa versa. In iTunes "Edit" "Perferences" "Advance" settings I have created a folder for my iPad, should I do the same with the iPhone? and change folders through the Advance when I sync up each device ? or would this confuse iTunes ?

How are you syncing your ipad right now?  Are you just syncing everything? You don't have to - you check off which items you want for the ipad. then when you get the iphone you check off different apps for that. This apple article has a screenshot of that in step #5
http://support.apple.com/kb/ht1977
If you're determined to have separate folders between your ipad & iphone, you might be better off having completely separate library database files. You can do a shift-start to choose between your iPad and iPhone library database and have them use different folders.
Switching the folder location in one library database is guaranteed to be a mess, no matter how you think you'll always remember. If you have podcasts that auto download they might start downloading when you're in the wrong library, for example.
itunes is designed to support multiple devices...maybe you're overthinking this?
The backups will still be separate though and always go to that location in the article I posted above.

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