That is because write_multi is meant for making animated images, like an animated tiff or animated gif. The first image is the one that is first in the animation stack.

What you want is the paste method. I have an example that shows what to do at Mirrored text with Imager. It pastes a mirror image side by side, but with a small amount of manipulation, you could make the code paste your 2 images top and bottom. You could resize your pasted images afterwards if desired. Read perldoc Imager::Transformations for more information and code.