Burning the midnight oil on this one big time. This is very slow and intensive, a lot more work than simply overlaying in GE, but better ultimately. Here are two illustrations: in GIMP and Qgis.
Otago Central Railway [47C]: CG aerials
Right now we are just at the level of putting in the base layer to draw the maps. The next thing is to put in a layer mask for each base image to control the transparency of the lake, in this case.