I assume you are interested in manifolds for a '69 SS350.
All w/manual trans had the AIR emission control system and used manifolds with cast-in bosses machined for the air inject tubes. Same manifolds used on the Z/28 [and others]; available in repro. Automatics did not use the AIR system and used manifolds that did not have provision for AIR. They are dimensionally the same as the AIR manifolds and will fit just fine. '69 Chevelle and Nova 350s also used the same manifolds.
That is essentially the difference between "auto" and "manual" manifolds but it really only applies to small-blocks for '69. All '69 Camaro BBs had AIR so manual and auto trans used the same manifolds.