How it normally works is:
1. The customer clicks the checkout button on the cart page.
2. Our app creates a discounted draft order then immediately takes the customer to checkout for the discounted draft order.
3. Once the customer completes payment, the draft order is converted in to a regular order in Shopify, and it's at this time that the order would likely hit your warehouse.
If your wholesale customers don't need to pay immediately (e.g., they have net-30 terms), you'd want to use our "Net orders" feature.
Instead of taking customers to checkout for the discounted draft order, they're instead emailed an invoice from Shopify allowing them to complete payment on the draft order at a later date.
Because it's still a draft order until payment is made, it would not hit your warehouse until the customer completes payment.
Shopify has details on draft orders here: