At this time the Nook reader for the iPad is designed for a single user only. There is a work-around but it is time consuming.
Here it is:
Log out by tapping on the settings button and then the Logout button in the resulting window. This will delete all of your books from that account from your device but not from your locker in the cloud, so while you won't be able to read those books from account 1 when you are logged in to account 2, if you log out of account 2 and back in as account 1 your books will be back on your device. Likewise, when you again log out of account 1 and back into account 2 all of your account 2 books will be back on your device.
Please contact Customer Support to suggest a Feature Request for the Nook reader app for the iPad.