I thought it would be easy, but I'm having trouble with layers too. I did get it to work saving the output as a gif, so I wonder if I don't have all the support libraries to write multi-layer psds.

#!/usr/bin/perl
use warnings;
use strict;
use Image::Magick;

my $image1=new Image::Magick;
$image1->Read("dir1/1.gif","dir1/2.gif");
$image1->Write("dir1.gif");
[download]

I'm opening this multi-layer-gif in gimp. I don't know if photoshop will open it the same way.

Update: .tif also works as a multi-layer file, at least you won't have to combine both images down to an 8 bit pallette.