You need iTunes, not the Apple Store, in order to update your iPad.
Connect the iPad to your computer with the cable.
Launch iTunes - if it does not start up on its own.
Click on your iPad's name under the device heading in the left sidebar of iTunes.
Click on the Summary Tab in the iTunes window on the right - at the top of the window.
Click on the Check for Update button.
If you are running iTunes 11 - and you can't see the sidebar - at the top of the screen go to View>Show Sidebar.
If you need iTunes, you can download the latest version here.
http://www.apple.com/itunes/