Go into iTunes, with your iPad connected, and in the left column click on your iPads name under "Devices". You will see a "Summary" screen come up with tabs across the top, click on "Apps" tab, you will see all of the apps you have bought or downloaded from Apple listed there. There general rule in iTunes is, if it's checked it will be synced, if it's not checked it will not be synced, or if it is already synced it will be deleted. You may want to uncheck the "Automatically sync new apps" box if you intend to have a lot of different apps on each device. You may also want to go to "Edit", upper left hand corner of iTunes, and click on "Preferences", goto the "Devices" tab and check the box by "Prevent iPods, iPhones, and iPads from syncing automatically". That way if you download an app in iTunes it won't automatically put it on your device when you connect, this allows you to select what you want to sync.
