Thw Ford Racing catalog has two different crossmembers, but they are for the width of the mounting brackets (where it bolts up to the body), and states that it is for "most" transmissions. I never heard of a difference between auto and manual crossmembers, I know they take the same trans mount. As far as installing either way, it will only go in one way as the trans mount will be way off of center, and the tall hump is on the passenger side.
Fred.