Well, I think that Altgens 6 might have been a planned, coordinated photo, specifically timed to show Kennedy being hit, and SS agents turning to look back toward the depository, the sole purpose being to capture a specific moment, as "proof" that Oswald fired shots from the depository. The "conspirators" knew that people would be analyzing evidence, and this would point them in the "right " direction, following the script.
As far as manipulation, I'm not a photographic expert, but some researchers(Groden, I believe) have said that there was some work done in front of the depository(colored in areas & matte lines) and in the 2nd floor of the Dal-tex building. It looks to me that the photo was manipulated. Exactly in what ways, I don't know.