while (<PERSON>)
{
chomp;
$dn = $ldap->search( #return only the employeeID DN
        base => "$BASEDN",
        filter => "(&(objectClass=user)(employeeID=$_))",
        scope => "sub",
        attrs => [@attr]
        );

        next unless $dn; # Make sure something is returned
while( my $entry = $dn->pop_entry() )
{
        $result->write_entry($entry);
        if ( $result != /dn:/ )
{
        print OUT (@lines);
}
while (<MGR>)
{
...

##</code><code>##

while (<PERSON>)
{
    chomp;
    $dn = $ldap->search( #return only the employeeID DN
        base => "$BASEDN",
        filter => "(&(objectClass=user)(employeeID=$_))",
        scope => "sub",
        attrs => [@attr]
        );

        next unless $dn; # Make sure something is returned
    while( my $entry = $dn->pop_entry() )
    {
        $result->write_entry($entry);
        if ( $result != /dn:/ )
    {
        print OUT (@lines);
    }
    while (<MGR>)
    {
    ...

##</code><code>##

my %manager;
while (<MGR>) {
    $manager{ $_ } = $ldap->search(...); # return only the manager DN
};

while (<PERSON>) {
    ... # you never seem to use the information from MGR here...
};