Yes, currently proposed orders are filed through CM/ECF. However, currently they are submitted just like any other document in CM/ECF (i.e., motions, responses, statements, etc.). This has several disadvantages such as taking up space on the docket sheet, less flexibility when processing orders, and lack of a means to track an order's progression through the system.
Uploading orders to E-Orders will look very similar to the way you upload orders now. This is because both E-Orders and the current method of submitting proposed orders use CM/ECF as the underlying mechanism for browsing and uploading orders. What differentiates E-Orders over the current method are the enhanced logistics involved in processing your order – from upload to review to signature to docket – and the benefits those logistics provide to both the court and the user.