Can I change Autoship orders on behalf of my customers?
WooCommerce has steadily been adding features that will eventually lead to a workflow for manually entering "phone orders" aka "manual orders" entered by a site Admin.
With Autoship, we've added Admin features, one of which allows you to manage a customer's Autoship on their behalf. You can do this by logging into your Wordpress Admin > Autoship > Customers and then selecting the "Autoship" link next to the customer you wish to make changes for.
However, this is strictly limited to Autoship schedules. There are a few plugins that we've seen store owners use to that enable a "shop as customer" experience in WooCommerce directly. This would be necessary to perform actions on behalf of customers outside of the Autoship schedules page (for example: a site admin changing a password or adding a payment method on behalf of a customer using the website).