$ cat 2
1
2
3
4

$ perl -i.orig -p -l -e "print 'three' if /3/" 2

$ cat 2
1
2
three
3
4

$ cat 2.orig
1
2
3
4

$ perl -MO=Deparse -i.orig -p -l -e "print 'three' if /3/"
BEGIN { $^I = ".orig"; }
BEGIN { $/ = "\n"; $\ = "\n"; }
LINE: while (defined($_ = <ARGV>)) {
    chomp $_;
    print 'three' if /3/;
}
continue {
    print $_;
}
-e syntax OK
[download]

So here is what I have. This just appends the end of the file which is close but not what I need. I need to add fileA in the MIDDLE of FileB

#!/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).

1. Open your output file (say fileC)
2. Open your fileB
3. Read through fileB file line by line, finishing if all lines have been read.
4. Have you reached the place of insertion? If no, print to your output file, the line just read and go back to 3. If yes, open fileA and print all of it to your output file.

use strict;
use warnings;

open my $FILEC, '>', 'fileC';
open my $FILEB, '<', 'fileB';
open my $FILEA, '<', 'fileA';

while (my $line = <$FILEB>) {
    do {local $_; print $FILEC $_ while (<$FILEA>)} if $line =~ m/INSE
+RT BEFORE HERE/;
    print $FILEC $line;
}
[download]

Of course you should add some tests to see whether opening of the files and writing to them succeeds.