It is situations like this that prompted Audioholics' misgivings about Atmos in the first place. Dolby Atmos is not simply additional channels. It is a sound mix scheme that can create discreet channels of sound based on the assumption that your speakers are correctly located. It does nothing for a system where the speakers are not positioned correctly. This is one of the reasons why I link to the
Atmos Home Installation Guide as much as I do. Atmos is attempting to create a certain kind of sound field. For a system where all the speakers are in the ceiling, that sound field can not exist. Adding Atmos speakers to a system like that will do nothing to improve the sound of that system.
The guys at speakercraft were jerking your chain, they will say whatever it takes to make a sale. If you want to make your system sound better, use speakers that are level with your ears. That will make your sound system a thousand times better than adding Atmos speakers.