my $confOut = $conf->XMLout($confIn, OutputFile => $xmlConf);
# ...
$confOut->{conf}->{lastRun} = $epoch;

##</code><code>##

use strict;
use warnings;

use XML::Simple; 

my $xmlConf = "file.xml";
my $conf    = new XML::Simple(
    NoAttr     => 1,
    KeyAttr    => [],
    ForceArray => [qw(box1 box2)],
    KeepRoot   => 1,
    SearchPath => "."
);

my $confIn = $conf->XMLin("$xmlConf");

printf "box 1: Username - %s, Password - %s\n",
  $confIn->{conf}->{box1}[0]->{username},
  $confIn->{conf}->{box1}[0]->{password};

printf "box 2: Username - %s, Password - %s\n",
  $confIn->{conf}->{box2}[0]->{username},
  $confIn->{conf}->{box2}[0]->{password};

my $epoch = time();

$confIn->{conf}->{lastRun} = $epoch;

$conf->XMLout( $confIn, OutputFile => $xmlConf );