Unfortunately due to the way the admin interface is currently coded, it makes it quite difficult for WooCommerce Wholesale Prices and Premium to modify the pricing on the fly for backend manual orders in WooCommerce.
We do however have a valid workaround which is to use the very good User Switching plugin by John Blackbourn. This plugin lets you assume the identify of another user on the site and do handy things like placing orders for them in WooCommerce.
One of our favourite suggestions is to use this in combination with the WooCommerce Wholesale Order Form plugin which makes for a very speedy and efficient ordering process that is fast enough to use over the phone.
Hope this helps!