To parse your layout CSV file, you could use one of the CSV CPAN modules, such as Text::CSV_XS. This would place your starting column positions into an array. A simple example is:

use strict;
use warnings;
use Data::Dumper;
use Text::CSV_XS;

my $csv = Text::CSV_XS->new();      # create a new object
while (<DATA>) {
    my $status  = $csv->parse($_);  # parse a CSV string into fields
    my @columns = $csv->fields();         # get the parsed fields
    print Dumper(\@columns);
}

__DATA__
aa,bb,cc
0,2,3
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which prints:

$VAR1 = [
          'aa',
          'bb',
          'cc'
        ];
$VAR1 = [
          '0',
          '2',
          '3'
        ];
[download]

Then, you could use the column positions to format your ASCII data file, by reading in the data line by line and adding commas as follows:

use strict;
use warnings;

my @cols = qw (5 11);
while (<DATA>) {
    chomp;
    my $row = '';
    my $start = 0;
    for my $cs (@cols) {
        my $offset = $start;
        my $length = $cs-$start;
        $row .= substr($_, $offset, $length) . ',';
        $start = $cs;
    }
    $row .= substr($_, $start);
    print "$row\n";
}

__DATA__
12345678901234567890
abcdefghijklmnopqrst
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this prints:

12345,678901,234567890
abcde,fghijk,lmnopqrst
[download]

Perhaps you could adapt these simple examples for your application.