First, iTunes keeps your iPads separate by it's UDID (or serial number). Or some other number - but it doesn't matter because it used some number to keep the iPads separate. So, you can have two iPad that you've named the same and iTunes will still know the difference. The actual naming of the iPad you do is solely for YOUR convenience, so you can tell between "Dippy's iPad" and "Dippy's Husband's iPad." So far, I've never had iTunes not know which one is attached (and I maintain 4 iPads with my iTunes)...
Now, to allocation.
When you first connect your iPad to iTunes, the first thing you want to do is right click (on the iPad tab) and select "Transfer Purchases." That'll tell iTunes of any downloads (to that iPad) you've made since the last time you connected the iPad to iTunes. This'll Make it so iTunes knows 100% what's on that iPad. I recommend making this a habit every time you connect either iPad.
Then, with the iPad connected, go to the Apps tab (across the top of the iTunes page, on the right). There you will see a list of all the apps in iTunes. In the column, on the right, you should see a button that reads either "Remove" or "Install." The ones installed on that iPad will be already ID'd by iTunes (they're the ones that read "Remove").
If you want to put an app on that particular iPad, click on one of the "Install" buttons and see how it changes to "Will Install." Once you have finished selecting the app(s) you want to put on that iPad, you can click the "Apply" button in the lower right of that Apps page. iTunes will then put those apps on that iPad. You can also do the same process in reverse to remove an app from that iPad (by clicking the Remove button and then clicking the "Apply" button).
iTunes is very good at keeping the iPads and their data/info separate. I hope this reassures (and didn't make the mud thicker!).
Yes yes yes....... thank you very much for all your info. I now have 2 iPads on the same account and as you say, it knows, by whatever means, which is mine and which is the grumpy old man's .......
Now I can sleep easy and drop the 'Dippy'!
Hi and welcome to the Forum!
So glad you now have your issue sorted with Marilyn's great advice.
If you do really want to drop the Dippy, let me know by PM (private message) and I will arrange this for you.
3 very informative threads from which you will learn many tips and shortcuts for the IPad.
iOS5 Tips and Tricks
Easy pictorial shortcuts & Helpful places. - For People new to the iPad.
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iPad 2 64gb wifi/Cellular - iPad Mini 32gb wifi/Cellular - iPhone 5 - Apple TV - MacBook Pro 15"