#!/usr/bun/perl
#------------------------------
# This script searches for "search"
# and adds lines from fileSource to fileOutput

use warnings;
use strict;

#use Fcntl (:flock :seek);

# Check
unless(-e $ARGV[0] || -e $ARGV[1]){
      print("Please Enter A Valid File Name\n");
   exit 1;
}
#if($ARGV[0] == "--help"){
#      print("Usage is:\n");
#      print("perl conference_add.pl <Source File> <Output File> <Sear
+ch String>");
#}

# assigns file path to local variables
my($fileSource) = $ARGV[0];
my($fileOutput) = $ARGV[1];
my(@inputLines);
# opens files for reading/writing
open(FILESOURCE, "<", $fileSource) || die("Can not open $fileSource $!
+");
open(FILEOUT, ">>", $fileOutput) || die ("Can not open $fileOutput $!"
+);

@inputLines = <FILESOURCE>;
print FILEOUT @inputLines;


close(FILESOURCE);
close(FILEOUT);
[download]

I'd do it like this:

#!/usr/bin/perl

use strict;
use warnings;

( @ARGV == 3 and -f $ARGV[0] )
    or die "Usage:  $0  primary.file  secondary.file  insertion_point_
+pattern\n";

open( my $in1, "<", $ARGV[0] ) or die "$ARGV[0]: $!\n";
open( my $in2, "<", $ARGV[1] ) or die "$ARGV[1]: $!\n";
open( my $out, ">", "$ARGV[1].including.$ARGV[0]" )
    or die "$ARGV[1].including.$ARGV[0]: $!\n";

while ( <$in2> ) {
    print $out $_;    # assuming you want content added after target p
+attern
    if ( /$ARGV[2]/ and $in1 ) {
        while ( <$in1> ) {
            print $out $_;
        }
        close $in1;
        $in1 = undef;
    }
}
[download]

You might want to include a couple of "rename" steps after the outer while loop (rename the old "secondary.file" to "secondary.file.old", rename the output file to "secondary.file").

Note that if the given pattern never matches anything in the secondary file, the primary file never gets read or added to the output (output will be identical to input).