1. Don't need parens when using "my" to declare a single variable - e.g.
   
   my $confINPUT;
   
   not:
   
   my($confINPUT);
   
   Similarly, do
   
   my ($confID, $confPIN)
   
   instead of:
   
   (my($confID), my($confPIN))
   
2. Don't escape characters that don't need escaping, like the underscores at line ~33.
3. You're inconsistent with operations that you check for failure. AFAIK it's pointless to check close() for failure when you've opened a file read-only. On the other hand, you aren't checking the result of your print() calls, which could fail.
4. "my $confINPUT" at approx. line 24 (file scope) is unused (shadowed by the same-named variable inside the while loop) - eliminate it.
5. Don't double-quote things that don't need string interpolation, like "$ARGV[0]". Just write $ARGV[0] directly.
6. Some of your comments don't match the code, like # close files for input and # open files for output.
7. Be aware that terminating your "die" messages with a newlines tells perl to not print the line number where the die occurs. This may be desirable if you want simpler error messages for end-users, but for debugging it's usually nice to see the line number.
8. You copy and unlink the input file while you still have an open file handle (CONF_ID) to it. *nix lets you do this, but it won't work on Windows.
9. You should check the result of the File::Copy copy() call. If the copy fails in your current code, you still blow away the original input file.

I'd refactor to something like this:

#!/usr/bin/perl

# Written By Jon
# This script takes CONF_IN and populates
# 3 templates which are then put into a final file all 
# together
# Usage: perl conf_add.pl
# requires:
# input: templates in templates folder
# input: list of conference IDs and conference PINs
#        with ID and PIN on one line in order.
# program outputs to file: conference_additions
# 
# TODO: Error handling when there are no entries in CONF_ID
# TODO: SCP files to server
# TODO: Random Number Generator
# TODO: Add insert.pl 

use strict;
use warnings;

use File::Copy ("cp");
use POSIX;

my $TEMPLATES_DIR = "templates";
my $FINISHED_DIR  = "finished_list";
my $OUTPUT_DIR    = "additions";

my $date = POSIX::strftime('%d_%b', localtime);

open(my $confid_fh, "<", $ARGV[0]) || die("$!\n");

my $i = 0;

while (my $line = <$confid_fh>)
{
    $i++;

    my ($confID, $confPIN) = split(" ", $line);

    process_template("conf_template1", "conf_list1.tmp", { XXXXXX => $
+confID });
    process_template("conf_template2", "conf_list2.tmp", { XXXXXX => $
+confID, AAAA => $confPIN });
    process_template("conf_template3", "conf_list3.tmp", { XXXXXX => $
+confID });
}

close $confid_fh;

open(my $confadd_fh, ">>", $OUTPUT_DIR . "/additions_$ARGV[0]_$date") 
+|| die("$!\n");

# adds 1st set of conf config to conf_additions
print $confadd_fh "; start conference config 1\n";
append("conf_list1.tmp", $confadd_fh);

# adds 2nd set of conf config to conf_additions
print $confadd_fh "\n\n; start conference config 2\n";
append("conf_list2.tmp", $confadd_fh);

# adds 3rd set of conf config to conf_additions
print $confadd_fh "\n\n; meetme_additional_custom.conf\n";
append("conf_list3.tmp", $confadd_fh);

close $confadd_fh;

# moves list to finished folder
cp($ARGV[0], $FINISHED_DIR . "/$ARGV[0].finished");
unlink $ARGV[0];


# deletes temporary files
unlink "conf_list1.tmp" || die("$!\n");
unlink "conf_list2.tmp" || die("$!\n");
unlink "conf_list3.tmp" || die("$!\n");

print "Number of Entries processed: $i\n";

exit 0;


sub process_template
{
    my ($tmplfile, $outfile, $substitutions_ref) = @_;

    open(my $out_fh, ">>", $outfile) || die("$!\n");

    open(my $template_fh, "<", $TEMPLATES_DIR . "/" . $tmplfile) || di
+e("$!\n");

    while (my $line = <$template_fh>)
    {
        while (my ($key, $value) = each %{$substitutions_ref})
        {
            $_ =~ s/$key/$value/g;
        }

        print $out_fh $_;
    }

    close $template_fh;

    close $out_fh || die("$!\n");
}

sub append
{
    my ($infile, $out_fh) = @_;

    open(my $in_fh, "<", $infile) || die("$!\n");

    while (<$in_fh>)
    {
        print $out_fh $_;
    }

    close $in_fh;
}
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