How to avoid duplicating files that goes on an iPad?
On a Mac: Drag the files into iTunes with the option key down and the files won't be copied to your iTunes Media folder.

That's the exact result you like.

There is also the option to change it so you don't have to press option key:  

You can press option key after changing that setting to copy it on purpose. (Exact opposite of default setting)

Good luck :)