Currently customers are associated with sales, but not with purchases/invoices. When sending data to QuickBooks, or any accounting solution, purchase transactions do not have a way to associate with a specific customer, making Job Costing or Profitability by Customer reports impossible.
As of the last release, COGS from inventory sales do associate with the customer, which is awesome. But other non-inventory purchases have no customer association. Adding an optional customer field to Purchases would solve this.