Indeed iTunes will recognize both devices.
Like jlblodgett said, iPhone apps go to both and iPAD apps only to the iPAD.
Also Music, books, photo's can be setup indepently for both machines.
For instance:
iPAD: I sync all photo's from my Aperture library.
iPod: Only the photo's rated with 5 stars.
iPAD: Only the 25 most played songs.
iPOD: Complete song library
There are some basic filters available, but of course it is possible to make your own filter criteria.