Just to wrap things up...
One iTunes on one login of one computer can support multiple iPads AND multiple Apple IDs.
When finished, iTunes for your login on your computer will contain all of the data for both iPads and both Apple IDs. You then have the ability to configure the sync characteristics separately for each one. Since one iPad can also support multiple Apple IDs, you can mix & match apps, music, etc. any way that you wish.
The only (minor) caution when you're using multiple IDs is a slight nuisance when it's necessary to update an app. You MUST have the password for the ID that was used for the original purchase. Also, the updating is slightly more difficult if done on the computer as you must change the ID for the update and then change it back when finished. If you update on the iPad, the iPad takes care of that for you but, of course, you still need the password.