Then they have no idea what they are talking about. There is no setting on the iPad to make iBooks default, or un-default it.
If you are unable to read a book bought from Barnes & Noble in the Nook app, then it is either a problem with the book or the app. You can not read an ebook purchased from Barnes & Noble in the iBooks app. The DRM (Digital Rights Management) is not compatible.
If you are somehow getting the book in the iBooks app, you are downloading it wrong. The book should be purchased on the Barnes & Noble website. It should then automatically show up in the Nooks' library with a big green download button on top. You tap that button to download the book.
You should not download it directly from the Barnes & Noble site via Safari or a link in Mail. If you do that, you will only be able to open the book in those apps that register themselves as compatible with the book's format. For whatever reason the Nook does not register itself as compatible with ePub files (while iBooks does) so it is not offered as an option when download by any method except inside the Nook app. Note, this is not because iBooks is default. It is because the Nook app is not registering itself. You can't fix that. The app developers need to do it. When/if the do the Nook app will show up in the list when you chose the Open In option.