... talk mainly about how to stick one big block of documentation at the top or bottom of the whole file...

That's one way of doing it (or looking at it) I guess, but what's to stop you from adding multiple blocks of POD?

#!/usr/bin/perl -w
use strict;

# codage...

=head1 NAME

  doStuff function

=head1 DESCRIPTION

  This sub is designed blah de blah blah
  and on and on etc ad infinitum

=cut

sub doStuff {
  # code for sub
}

# codage...

=head1 NAME

  What the next line does

=head1 DESCRIPTION

  This line uses some funky techniques I picked
  up from PM and does the following...

=cut

# insert incredibly funky bit of perl code here

# carry on coding...
[download]

HTH, if not lemme know and I'll try to anser any more q's you have