Let's assume for a second i knew which object are in the back, even then, how do i need to draw this? I've added my code.

use GD;
use constant PI    => 4 * atan2(1, 1);
$im = new GD::Image(400,400);
$black = $im->colorAllocate(0,0,0);
$red=$im->colorAllocate(255,0,0);
$green=$im->colorAllocate(0,255,0);
$im->filledEllipse(200,200,50,50,$red);
$im->filledEllipse(300,200,25,25,$green);
for($xy=0;$xy<6.28;$xy+=0.01){
$x = 100*cos($xy);
$y = (43.75/2)*sin($xy);
push @punten,[200+$x,200+$y];
    }
$data =$im->gifanimbegin(1,0);
$data.=$im->gifanimadd(1,0,0,1);
    
for($z=0;$z<=$#punten;$z+=20){
$ima = new GD::Image(400,400);
$black = $ima->colorAllocate(0,0,0);
$red=$ima->colorAllocate(255,0,0);
$green=$ima->colorAllocate(0,255,0);
$ima->filledEllipse(200,200,50,50,$red);
$xc = $punten[$z][0];
$yc = $punten[$z][1];
$ima->filledEllipse($xc,$yc,25,25,$green);
$data.=    $ima->gifanimadd(1,0,0,1);
    }    
$data.=$ima->gifanimend;
binmode STDOUT;
print $data;
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Instead of drawing $red and then drawing $green, you need to find out which of the two is in the back, and draw that one first.

For example, do it like this:

# Define the two planets
my @large= ($red,   200,200,50,50 );
my @small= ($green, $xc, $yc, 25, 25 );

my( $front, $back );

if( $red_is_in_front_of_green ) {
    $front= \@large;
    $back= \@small;
} else {
    $front= \@small;
    $back= \@large;
};

# Just in case we ever go beyond two objects
my @objects_to_draw= ($back, $front);

for my $item (@objects_to_draw) {
    my( $color, @position )= @$item;
    $ima->filledEllipse( @position, $color );
};
[download]

Thank you.