Apps in iTunes syncing to both iPhone and iPad

I have had an iPad for several months now and have accumulated a number of apps both iPad specific and general apps for both the iPad and iPhone - as broken out in the app portion of my iTunes. I just purchased an iPhone, and my question is, do I have to have all the apps in iTunes transferred to both devices?
In an ideal world, I would have one set of apps only on my iPad and another set of apps on my iPhone.
I understand that the iPad specific apps will not transfer to the iPhone.
For example, I would like to have the GQ magazine app on my iPad, but not my iPhone. Is this possible?
And a subsidiary question, if I download an app via the iPhone, when I sync it with iTunes, will the app show up on the iPad next time I sync the iPad with iTunes? (Same with deleting apps).
Thanks for your help.
MacBook Pro