How can I make sure that coupon codes don't also apply to wholesale orders?
You can disable the coupon code input field for the wholesale orders from the Wholesale All In One application dashboard. Please follow the below steps.
From the application dashboard, go the the 'Settings' section:
From the 'General' tab, uncheck the box called 'Enable additional coupon code field at cart page'
The coupon code input field has been removed from the cart page for wholesale orders and wholesale customers wouldn't be able to apply Shopify discount code to avail additional discounts. Please see the screenshot below as reference.