At this time, you will not be able to use automatic or manual discounts for wholesale orders, including applying then manually to drafts. Retail customers will still be affected by your automatic and manual discounts, only wholesale is unable to use extra discount codes.
In order to reduce confusion from your customer's side, we've removed the 'Discount Code' box from wholesale checkout.
In addition to Shopify's discount codes being unusable, you'll also be unable to use codes from other apps or programs for your wholesale customer's orders.
Your retail customers will be unaffected by this, so they will still be able to use discounts on their orders that are created outside of our app.