Yeah, I pretty much have to do the same with my television. There is a 3D button on the remote that has six options including SBS to choose from. I've cycled through them all just to be sure, but none of them seemed to work correctly. When I pick SBS the two images are not overlapping correctly. For some strange reason if I put my TV on 3D without selecting side by side I get a 3D image of both left and right screens separately. I have a Samsung 55C7000 if that makes any difference.
Edit: Problem solved. I was using a laptop hooked up to my television in single screen mode. I changed it to 2 screens dragged XBMC over to the second screen (TV) and that solved the problem. I'm guessing my television had a problem with whatever resolution single screen mode displayed on it.