It's quite easy to do this. With your iPad connected to your computer, click on the iPad name in the left hand pane then make sure that any auto syncing on iTunes is switched off in the main window. It's then just a matter of going through each of the tabs at the top of the iTunes window and using the manual manage/sync options on each page. As you switch them to manual then more and more options will become available to you on the screen.
It's really just a matter of playing around with iTunes on your desktop until you have it how you want it. Hope that helps you.