Hi,
Not confirming the order directly after the checkout when the customer select the bank transfer payment method is how it works by default.
And you can also manually validate the orders in the backend.
There is no system to have the customer upload a file for his order.
But you could create a contact form on your website with an upload field (you'll find many contact form extensions on the Joomla Extensions Directory for that) and an input field where the customer could enter his order number so that you would get an email and you could then just review the information and confirm the order.
