container.php

<?php

$di->set('db1', function() {
     return new \Phalcon\Db\Adapter\Pdo\Mysql([
        "host" => "localhost",
        "username" => "",
        "password" => "",
        "dbname" => ""
    ]);
});


$di->set('db2', function() {
     return new \Phalcon\Db\Adapter\Pdo\Mysql([
        "host" => "localhost",
        "username" => "",
        "password" => "",
        "dbname" => ""
    ]);
});

model.php

<?php
public function initialize(){
    //puedes conectar a la base de datos que desees
    $this->setConnectionService('db1');
    //$this->setConnectionService('db2');
}