The backup only restores the content of your apps and a few other things. To actually restore the apps, plug the iPad into iTunes, select it, go to the Apps page, and make sure they are set to sync. Then sync.
If for some reason your apps are not on iTunes in the computer, because you never transferred them, you'll have to go to the App Store on the iPad and download them again. You won't be charged for re-downloading them. Hopefully you remember what all the important ones were.
If you want to back them up on iTunes when you are done, right click on the iPad under devices when it is connected. Choose Transfer Purchases, and everything you've bought on the iPad will be copied to the iTunes library on the computer.