All Gerber software has an align layers function, you pick a feature on the base layer (say a pad), then a feature on the layer you want to align, and the align layer will be moved so the feature you picked is at the same x,y position as the feature on the base layer.
I have never mirrored layers when reading them into a Gerber manipulation package (Camtastic, CAM350 etc), or produced one mirrored from the CAD package. Always produce data as viewed from the top (primary) layer.