To combine two images of the same size with ImageMagick, you simply do the following:

The following will overlay overlay.png on top of output.png

mogrify -draw "image SrcOver 0,0 0,0 'overlay.png'" output.png

While this one will overlay overlay.png on top of input.png and save it as output.png

convert input.png -draw "image SrcOver 0,0 0,0 'overlay.png'" output.png

You can download imagemagick from http://www.imagemagick.org/