This is certainly not what you want:

                    'Waypoint' => [
                        "@waypoints"],
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The double quotes will stringify the array which completely removes the array structure. Also, I just noticed that you have a problem in the way your construct @waypoints:

push(@waypoints, "{'Longitude' => '$point[0]', 'Latitu
+de' => '$point[1]', 'SequenceNumber' => '$count'}");
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You don't want double-quotes (or need single quotes) here either:

push(@waypoints, { Longitude => $point[0],
                   Latitude => $point[1],
                   SequenceNumber => $count } );
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Combined with the not using stringification should get you pretty close to what you want.

Update: Here's some code that seems to produce what you want:

use strict;
use warnings;
use XML::Simple;

my $xml = new XML::Simple (
  RootName => 'Task',
  XMLDecl => '<?xml version="1.0" encoding="UTF-8"?>',
);

my @waypoints = (
  { Long => 1, Lat => 2, SeqNo => 1 },
  { Long => 3, Lat => 4, SeqNo => 2 },
);

my $waydata = {
   'xmlns' => "http://Task.CUIntegration.com",
   'xmlns:xsi' => "http://www.w3.org/2001/XMLSchema-instance",
   'xsi:schemaLocation' => "http://Task.CUIntegration.com Task.xsd",
   'ID' => ['ID'],
   'Type' => ['Loop'],
   'Destination' => ['Velocity'],
   'Waypoint' => [ @waypoints ],
};

print $xml->XMLout($waydata);
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