theme ALL form elements in a tpl through hook_preprocess_HOOK
I am not sure if this is what you are trying to do. But from the question I feel that you just want to re arrange the form in an order of your choice.

The best place to do that is with in a hook_form_alter function. Rather than the preprocess_HOOK.

Every form element has a property called #weight This could be used to arrange the forms in order the one with higher weight would go down.