If I understand you correctly, you have apps in iTunes (on your computer) but not on the iPad? I'm going to assume the answer to that question is "yes." So, there are two ways to get those apps to your iPad.
(1) Connect your iPad to iTunes (via USB). When you see the iPad appear in the left column, right click on that line and select 'transfer purchases." This step is so that your iPad can tell iTunes what's loaded on it (so iTunes won't try to remove apps that are in it's records as being on the iPad).
Then, press the Apps tab in iTunes (on the right side, across the top). Locate the app(s) you want to put on the iPad and ensure they have a checkmark next to them. Once you have checked all the apps you want to put on the iPad, press the "Apply" button at the bottom right side of the iTunes screen. iTunes will do its magic and load those apps onto your iPad.
Or, you can do it all from the iPad (this is best if you only have one or two apps to put on the iPad)...
(2) On the iPad, go to the App Store icon. After you've opened the store, either go to the Purchases tab and locate the app(s) you want to install or find them by using the search function. Once you've located the app(s), they should have an "Install" button next to them. Press the button and they will begin to install (you will have to put in your password if you are on iOS 5.x or lower). That's it, they are then on your iPad.
Hope this helps. If I've made a bad assumption about your issue, please let me know and we'll take another shot at it.
Marilyn
