Assist cleaning up messy HTML/PHP code

WKS is right, first of all you should split your layout from your logic and your logic from your database query. (see Model-View-Controller-Pattern)

Lets start with your model (Model.php): (actually you could split it in a model for each entity/database table)

<?php
class Model()
{
     public function __construct(PDO $connection)
     {
         $this->connection=connection;
     }

     public function getZones($week)  //find a nicer name
     {
         //... see Peters post for a sample join
         // prepare multi dimensional array as needed in your template
         return $zones;
     }
}

It is in general a bad idea to run SQL queries in a loop, so try to create one join for all your queries.

Now the simple Controller (index.php)

<?php
require 'Model.php';
$connection=new PDO(...);
$model=new Model($connection);
$currentWeek = ...;
$zones= $model->getZones($currentWeek);

include "view.php"

That's it! Nothing fancy. Now the view:

<table>
    <tr>
         <th>Zona</th>
         <th>Baptismos Mulheres</th>
         <th>Conf. Mulheres</th>
         <th>Batismos Homems</th>
         <th>Conf. Homems</th>
    </tr>
    <?php foreach($zones as $zone):?>
    <tr>
         <td><?php echo $zone['name']; ?></td>
         <td colspan="4"></td>
    </tr>                   
        <?php foreach($zones['areas'] as $area):?>
        <tr>
            <td>
                 <?php $area['name']; ?> <?php echo $area['companions']; ?>
            </td>
            <td colspan="4"></td>
        </tr>
        <?php endforeach?>
    <?php endforeach?>
</table>

Don't use all-capital-letter variable names. And don't use global variables. Both is considered bad practice.

First things first

Create two model classes:

<?php

class Zone {
    public $Name;
    public $ID;
    public $Areas = array();

    public function __construct($id = NULL, $name = NULL) {
        $this->Name = $name;
        $this->ID = $id;
    }
}

class Area {
    public $Name;
    public $ID;
    public $Companions = array();

    public function __construct($id = NULL, $name = NULL) {
        $this->Name = $name;
        $this->ID = $id;
    }
}

Then you have to clear your SQL statements becouse you are running to much query against the database while you can fatch all data with only 2 query.

SQL

First the companions:

<?php

$companionsResult = $PDO->query("SELECT CONCAT(title, ' ', mission_name) as MissName, area.uid AS AreaID
FROM missionarios
INNER JOIN missionary_areas ON missionary_areas.missionary = missionarios.mid
AND semana = '".$CONF->getSetting('current_week')."' AND area.uid IN (
    SELECT areas.uid AS AreaID
    FROM zones
    INNER JOIN areas ON areas.zone = zones.uid
    WHERE zones.active = 1
)'";

$companions = array();
foreach ($companionsResult->fetchAll(PDO::FETCH_CLASS) as $c) {
    if (!isset($companions[$c->AreaID])) {
        $companions[$c->AreaID] = array();
    }

    $companions[$c->AreaID][] = $c->MissName;
}

Zones and areas with merging areas with companions:

$zonesResult = $PDO->query(
                "SELECT zones.name AS ZoneName, zones.uid AS ZoneID, areas.name AS AreaName, areas.uid AS AreaID
                FROM zones
                LEFT JOIN areas ON areas.zone = zones.uid
                WHERE zones.active = 1");

$zones = array();

foreach($zonesResult->fetchAll(PDO::FETCH_CLASS) as $zoneres) {
    if (!isset($zones[$zoneres->ZoneID])) {
        $zones[$zoneres->ZoneID] = new Zone($zoneres->ZoneID, $zoneres->ZoneName);
    }

    $area = new Area($zoneres->AreaID, $zoneres->AreaName);

    if (isset($companions[$area->ID])) {
        $area->Companions = $companions[$area->ID];
    }

    $zones[$zoneres->ZoneID]->Areas[] = $area;
}

Result

var_dump($zones);

HTML

After viewing the results you can create your own view to display the date without having queries and other not view related stuff between your HTML stuff.

(I'm sure that i have made some typos in the code but it should work after some fix.)