Syncing any content works the same way. If you are running iTunes 11 - from the menu at the top of the screen - go to View>Show Sidebar. Once you can see the sidebar in iTunes, you should see your iPad under the devices heading when it is connected to your computer. After you click on your iPad name under the devices heading - all of the iTunes tabs should appear at the top of the screen on the right side of the iTunes window.
Then you can click on each tab - Summary, Info, Apps, Music, Photos, Movies, Books, Podcasts - whatever you want to sync from that section of iTunes - and you select the content to sync to the iPad. Using Aps as the example and starting from the beginning....
Connect the iPad to the computer and launch iTunes.
Click on the iPad name on the left side under devices.
Click on the Apps Tab on the right.
Click on Install next to all of the Apps that you want to sync.
Click on the Sync Apps Heading in order to select it.
Click on Apply in the lower right corner of iTunes.
You can do this same thing in each tab in iTunes to select your content. If you are auto syncing, you can let the iPad sync and then go through all of the steps above after the auto sync in order to select any content that did not sync.