So since it returns some of the emails then the ones that it doesn't return it messes up the formatting.

Also, what I want it to do is return the names of the people if an email address was not found.

I'm afraid I really don't understand what your problem is.

Ok I almost have it; however, when I run the script shown below when it finds more than one user with the same name it just prints one email address for each one and not each one for each user.

For instance:
It returns:
User - Email
Smith, Joe - Joe.Smith@perlmonks.com
Smith, Joe(2) - Joe.Smith@perlmonks.com
instead of:
User - Email
Smith, Joe - Joe.Smith@perlmonks.com
Smith, Joe(2) - Joe.Smith2@perlmonks.com
[download]

#!perl

use Getopt::Long;
use Net::LDAPS;
use Text::CSV;

($domainCont, $surNm, $givenNm, $dispNm, $eNo, $outFlNm, $id, $pw) = (
+'', '', '','', -1, '', '', '');

&GetOptions('dc=s'  => \$domainCont
           ,'i=s'   => \$id
           ,'p=s'   => \$pw
           ,'d=s'   => \$baseDir
           ,'f=s'   => \$inFlNm);

my $ad = Net::LDAP->new($domainCont) or die "Can't connect to AD >$!<\
+n";
$ad->bind($id, password=>$pw) or die " bind for $id failed >$!<\n";

my $base = 'OU=People,OU=staff,DC=ad,DC=wjgilmore,DC=com';
my $attrs = "sn, givenname";

open IN, "<"."./$baseDir/$inFlNm" or die "Can't open transfers file >$
+inFlNm<\n";
$outFlNm = "test.csv";
open OUT, ">"."./$baseDir/$outFlNm" or die "Can't open transfers file 
+>$outFlNm<\n";
print OUT "Name,,,Assistant\n";

while(<IN>){
    @mngr = split(/"/, $_);
    @manager = split(/, /, $mngr[1]);
    $mFName = "$manager[1]"; 
    $mLName = "$manager[0]"; 
    @assist = split(/,/, $mngr[2]);
    @assistant = split(/ /, $assist[1]);
    chomp($assistant[1]);
    $aFName = "$assistant[0]";
    $aLName = "$assistant[1]";
    $lenMFName = length($manager[1])*.5;
    $lenAFName = length($assistant[0])*.5;
    substr($manager[1],-$lenMFName)=$pmFName;
    substr($assistant[0],-$lenAFName)=$paFName;

    $filter1 = '(&(sn='.$mLName.')(givenname='."$manager[1]*".'))';
    $filter2 = '(&(sn='.$aLName.')(givenname='."$assistant[0]*".'))';
    my $results1 = $ad->search(base=>$base,filter=>$filter1,attrs=>$at
+trs);
    my $results2 = $ad->search(base=>$base,filter=>$filter2,attrs=>$at
+trs);
    $x1 = $results1->count();
    $x2 = $results2->count();
    
    if($x1 > 0){
        foreach $adEnt ($results1->entries){
            my $entry1 = $results1->entry($i1);
            my $mail1 = $entry1->get_value('mail');
            foreach $adEnt ($results2->entries){
                print OUT "$mFName,$mLName,";
                print OUT "$mail1,";
                my $entry2 = $results2->entry($i2);
                my $mail2 = $entry2->get_value('mail');
                print OUT "$aFName,$aLName,";
                print OUT "$mail2,\n";
            }
        }
    }
    else { 
        if($x2 > 0) {
            print OUT "$mFName,$mLName,Not Found,";
            foreach $adEnt ($results2->entries){
                my $entry2 = $results2->entry($i2);
                my $mail2 = $entry2->get_value('mail');
                print OUT "$aFName,$aLName,";
                print OUT "$mail2,\n";
            }
        }
        else {
            print OUT "$mFName,$mLName,Not Found,$aFName,$aLName,Not F
+ound";
        }
    }
}
$ad->unbind;
[download]

First I'd add use strict; use warning;. At the very least, $i2 is not defined.

Second, I'd add a "\n" at the end of print OUT "$mail1,";

Third, I don't see how the code you posted writes what you say it did. (I don't, for example, see hyphens in any of your prints.)