Hi,
You want to overlay the tiff files is it? The one is the background the other the foreground layer? Imagemagick is the right tool. There is also a command line program called 'convert' which can be used. You do not need a Perl script for this as long you do not need to do more than just the image manipulation.
Google gives you the following link when you search for "image magick overlay". The command described there should do the trick.
http://www.randomsequence.com/articles/overlaying-images-with-imagemagick/
If you need to do it with Perl/Image::Magick than I'm sure that this package gives you all the options the command line tool gives you. Just check the manual how to do it exactly.
Best,
Martin