I don't really care where the seam goes, and often I piece the back to the point that it's almost like a top so the seams go all over.
I have heard that there shouldn't be a seam in the center, but I don't understand why. Why would there be more stress in the center of a quilt? Are people playing tug-of-war with it? Even if they were, won't the quilt break at the weakest link, which could be off-center? (Just teasing of course.) My feeling is that after the quilt is quilted, any seams are pretty much hidden and are certainly stabilized. If it mattered at all on a bed quilt (say you thought the area with the seam might be rougher), wouldn't you want that seam in the center so that neither person under the quilt would be directly under the seam?
As far as longarming, I just turn the quilt so that the main seams are horizontal while the quilt is on the frame. It does make the backing lay better that way. I don't care whether the quilt is right-side-up, upside-down, or sideways on the frame. I understand that some designs might be easier to quilt if the quilt is in a certain orientation, but most of the time it wouldn't matter (and it never matters for the quilting I do).
I do care about how the fabrics on the back look if I'm using multiple fabrics there, and I try to arrange them in a pleasing manner, but if there's just one fabric, I just make sure I don't have a seam so close to the edge of the quilt top that it will cause problems when I trim the backing and start to bind it.