You can use Wholesale Club to apply discounts to draft orders you create manually in your Shopify admin.
Navigate to Orders in your admin, and click Create order to create a new draft order.
Add products to the order, and manually add any applicable taxes or shipping. This Shopify guide has instructions on filling out a draft order.
Note: Make sure you add products that are included in the wholesale discount rule you'll be using.
Using the Customer panel in the top right, search for your wholesale customer's profile. Select your customer, then save the draft order.
Tip: You can click on the customer to make sure they have the correct wholesale tag.
Click on the More actions dropdown menu and select Apply Wholesale Discounts.