Custom Checkout page
Well it might seem a little noobish mistake but nevertheless, for everyone that is interested out there.

After a lot of research I found out how to make it.

The problem that arises when you try to render a form in a .tpl file is the functionality of the form.

I was trying to render $page['content']
and I couldn't do the above.

So I had to add to MYTHEME\template.php these lines:

function MYTHEME_theme($existing, $type, $theme, $path) {
  return array(
    'commerce_checkout_form_checkout' =&gt; array(
      'render element' =&gt; 'form',
      'template' =&gt; 'commerce-checkout-form-checkout',
      'path' =&gt; drupal_get_path('theme', 'MYTHEME') . '/template/forms',
    ),
  );
}


and then I created: commerce-checkout-form-checkout.tpl.php in
MYTHEME/template/forms

and I just put this code inside:

&lt;div class="row"&gt;
  &lt;div class="col-sm-12"&gt;&lt;?php print render($form['cart_contents']); ?&gt;&lt;/div&gt;
&lt;/div&gt;
&lt;div class="row"&gt;
  &lt;div class="col-sm-6"&gt;&lt;?php print render($form['customer_profile_billing']); ?&gt;&lt;/div&gt;
  &lt;div class="col-sm-6"&gt;&lt;?php print render($form['commerce_payment']); ?&gt;&lt;/div&gt;
&lt;/div&gt;
&lt;?php print drupal_render_children($form); ?&gt;


The key to render the form right was the last line: 

&lt;?php print drupal_render_children($form); ?&gt;


which rendered all the missing funcionality (like ajax and submit buttons) from the form.

I hope this will help someone in the future to avoid all the time and hassle..