Here's a self-contained runnable version of the code I posted in Re: Appending data to large files.

my $record_end = qq{\$\$\$\$\n};
while (<DATA>) {
    next if ( $_ ne $record_end );
    print "--CSV stuff--\n";
}
continue {
    print;
}

__DATA__
example 1
example 2
END
$$$$
example 3
example 4
END
$$$$
[download]

Here's the output:

example 1
example 2
END
--CSV stuff--
$$$$
example 3
example 4
END
--CSV stuff--
$$$$
[download]

Unless I've misunderstood your requirements, this is putting the CSV stuff right where you want it.

Integrating that with the CSV-handling code I posted in Re^3: Appending data to large files (and the rest of your program, of course) is up to you.

As for your question about headers, a quick look at the Text::CSV_XS documentation reveals a column_names method. That's what I'd try first. If that doesn't work out, then maybe a longer quick look would be required.