First don't use the prompters in front of the cameras. Set each prompter glass to the best height for eye lines. The only challenge is if you're shooting over the shoulder shots. That's where it will look like they are not conversing with each other. So I'd avoid that. Perhaps you can shoot some cutaways later on with each person giving a short line and also some reaction shots with the other person's head and shoulder in the shots.
If there are real actors, they should be able to memorize a few sentences here and there to make it work.
TelePrompters make anyone other than very experienced teleprompter users sound like they're using a teleprompter.
The script also becomes VITAL in a situation like this. Nobody can sound and look natural - no matter how experienced an actor they are - when forced to say: "The new hybrid multi-combustible space heater from Aero Dynamics corporation is exactly what I was looking for to heat my fishing cabin." Somebody in charge has got to be experienced enough to write something like "Gotta new heater for my cabin. Finally didn't freeze my butt off last weekend." and do the branding with the visuals or a separate spokesmonkey. (Term used with love since I've done a fair bit of that over my career.)
Writing for the ear rather than the eye. It's a thing.
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Instead of actual prompters, flatscreen monitors or even video projectors can be used for the sightlines.
Another way to go is to use ear prompters and pre-recorded tracks that the actors just have to hear and repeat. This has the advantage of locking in the timing. It also, thru phonetics, lets people speak in foreign languages without actually knowing the language.
Thanks for the great insights guys. I am going to be using flat screen monitors positioned behind and to the side of the talents heads so hopefully the eye lines will look close.
The in ear prompter is a brilliant idea!
It will be a 3 camera shoot. Using the canon c100 mk2 with 24-70. The wide i think will be the hardest shot. But I'm hoping at 70mm if I pull back enough the image will be compressed enough that it will appear that they are looking directly at each other.