$section = $newQuote->getSection("1");

for ($i = 0; $i < sizeof($prebuildIDs); $i++){
    $departments = $section->getDepartments();
    $deptExists = false;
    $id = $prebuildIDs[$i];
    $name = $prebuildNames[$i];
    $department = $prebuildDepartments[$i];
    $qty = $prebuildQTYs[$i];
    if ($qty != 0){
        foreach ($departments as $dept){
            if ($department == $dept->getDepartmentID()){
                $depSecID = $dept->getDepSecID();
                $costCentre = $dept;
                break;
            } else {
                $deptExists = false;
            }
        }
        if (!$deptExists){
            $costCentre = $section->addDepartment($department);
            $costCentre->clearLabour();
        } else {
            $section->getDepartment($depSecID);
        }
        //Now add the prebuild to the department
        $item = new DepartmentPrebuildItem($id);
        $item->setQuantity($qty);
        $costCentre->addItem($item);
    }
}