First of all, you build HTML inside your script, not in the template - if you do that, there's no need for a templating system.

You have to prepare the data inside your script:

my @checkboxes = ();
my $checked = 3;
for (1 .. 5){
    my %rowh = ( 
         name        => "desc_$_" ,
         description => "description ($_) ",   
    )
    if ($checked == $_) {
        $rowh{checked} = 1;
    }
    push @checkboxes, \%rowh
}
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And in the template:

<TMPL_LOOP NAME=CHECKBOX_HEADER>
    <input type="checkbox" name="<TMPL_VAR NAME=name>" 
    <TMPL_IF NAME=checked>checked="checked"</TMPL_IF>>
    <TMPL_VAR NAME=description</TMPL_VAR></input>
</TMPL_LOOP>
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