iTunes manages each device separately. First, give the iPads different names so you can tell them apart, even though iTunes already knows. Do this on the devices themselves. Then, plug both in to the computer separately and you should have the devices available separately, although now iTunes shows them in this stupid device selector that barely looks like a selector at all. It's a button that has an icon for the device and, again, with the latest screw-up of the iTunes UI you may not notice it. Click on it and you should see two iPads in a drop-down menu. Select the old one and select music, photos, etc to remove those ones you don't want.
I really think your problem here might be mainly due to the iTunes UI.