I've never used Imager before :) This seems to work

#!/usr/bin/perl --

use strict;
use warnings;

use Imager;

# setting Imager::Color->new($red, $green, $blue, $alpha);
my $blue = Imager::Color->new( 0, 0, 255, 255);
my $red = Imager::Color->new( 255, 0, 0, 63);

my $canvas_blue = Imager->new(xsize=>700, ysize => 500, channels => 4)
+;
$canvas_blue->box(color => $blue, xmin=>10, ymin=>30, xmax=>200, ymax=
+>300, filled=> 1);

my $canvas_red = Imager->new(xsize=>700, ysize => 500, channels => 4);
$canvas_red->box(color => $red, xmin=>50, ymin=>80, xmax=>250, ymax=>3
+50, filled=> 1, alpha => 1);


my $outfile = "foo.png";

# overlay
$canvas_blue->rubthrough( src => $canvas_red );
$canvas_blue->write(file=>$outfile) or die $canvas_blue->errstr;
[download]

canvas, overlay, alpha, Imager::Transformations