You have to add a unique email address on each device. Under settings -> Facetime you will see "You can be reached at:"
Whatever email address you put in, it will send a confirmation message to that email with a link. Open link, put in your apple id and password and it will say something like "verified" or validated.... something like that.
Whatever device you added it to, the other device will beep twice. First to let you know that your other iPad just added a new email to it. The second asking if you want to add this email to this device. Select NO. If you hit yes on accident, no worries.... settings -> Facetime and uncheck the email address. (do not delete it, it will disappear from both.)
Now you have to do the same thing on ipad #2.
Something you can give a try... if you have way more than 2 devices (I've got about 10 now), and you have a gmail account, use that. For a unique email, put a plus after your username and a variable...
firstname.lastname@example.org your ipod will still route the verify email to you... and the +variable isn't a new email address that you have to keep track of.
Hope that helps.