code.php

<?php

        $dept = $this->em->getRepository('Common\Model\Department')->find($data['id']);
        $data = $form->getValues();

        if (isset($data['locations'])) {
            $locations = array_flip($data['locations']);
            foreach ($dept->getLocations() as $deptLoc) {
                if ($dept == $deptLoc->getDepartment()
                    && isset($locations[$deptLoc->getLocation()->getId()])
                ) {
                    unset($locations[$deptLoc->getLocation()->getId()]);
                    continue;
                }

                $dept->getLocations()->removeElement($deptLoc);
            }

            foreach ($locations as $locationId => $junk) {
                $location = $this->em->getReference('Common\Model\Location', $locationId);
                $dept->addLocation(new \Common\Model\DepartmentLocation($dept, $location));
            }
        }

Department.php

<?php

namespace Common\Model;

use Doctrine\Common\Collections\ArrayCollection;

/**
 * @Entity(repositoryClass="Common\Model\Repository\DepartmentRepository")
 * @Table(name="department")
 */
class Department extends AdminEntity
{
    /**
     * @Id
     * @Column(type="integer", name="department_id")
     * @GeneratedValue
     */
    protected $id;

    /** @Column(type="string",length=45,unique=true) */
    protected $name;

    /**
     * @Column(type="boolean", name="is_active")
     */
    protected $active = true;

    /**
     * @Column(type="string", length=45, name="cost_center")
     */
    protected $costCenter;

    /**
     * @ManyToOne(targetEntity="DepartmentType", inversedBy="departments")
     * @JoinColumn(name="department_type_id", referencedColumnName="department_type_id")
     */
    protected $type;

    /**
     * @ManyToOne(targetEntity="Site", inversedBy="departments")
     * @JoinColumn(name="site_id", referencedColumnName="site_id")
     */
    protected $site;

    /**
     * @ManyToMany(targetEntity="Smodule", inversedBy="departments")
     * @JoinTable(
     *  name="smodule_department",
     *  inverseJoinColumns={
     *      @JoinColumn(name="smodule_id", referencedColumnName="smodule_id",onDelete="cascade")
     *  },
     *  joinColumns={
     *      @JoinColumn(name="department_id", referencedColumnName="department_id",onDelete="cascade")
     *  }
     * )
     */
    protected $smodules;

    /**
     * @OneToMany(targetEntity="DepartmentLocation", mappedBy="department", cascade={"persist", "remove"}, orphanRemoval=true)
     */
    protected $locations;


    public function addLocation(DepartmentLocation $deptLoc)
    {
        if ($this->locations->contains($deptLoc)) {
            return $this;
        }

        $this->locations->add($deptLoc);

        return $this;
    }
}

DepartmentLocation.php

<?php

namespace Common\Model;

use Doctrine\Common\Collections\ArrayCollection;

/**
 * @Entity
 * @Table(name="department_location")
 */
class DepartmentLocation
{
    /**
     * @Id
     * @ManyToOne(targetEntity="Department", inversedBy="locations")
     * @JoinColumn(name="department_id", referencedColumnName="department_id")
     * @var Department
     */
    protected $department;

    /**
     * @Id
     * @ManyToOne(targetEntity="Location", inversedBy="departments")
     * @JoinColumn(name="location_id", referencedColumnName="location_id")
     * @var Location
     */
    protected $location;

    /**
     * @Column(type="boolean", name="is_default")
     */
    protected $isDefault = false;
}