The devices will stay in synch (including last page read), if they under the same account. This is supposed to be a feature. You can "archive" your books and they will not be downloaded to a device (I think), but then they would be archived for all devices on that account. I do not think there is any way to pick and choose.
One way to handle this would be to register the new device as a different user (different email/user name) but with the SAME credit card number. This would make it look as though you were a family member and under the B&N family arrangement. Then you could, I think, pick and choose which books to download - free - to each device.