The markup to be added to invoices is added to the expense form.  When you make the expense, pay your sub, and add the markup on the expense page.  Then you create an invoice, and the expense(with the markup) is shown on a menu on the right-hand side of the screen, and then you just click "add".  Then you track your employee's time in QuickBooks time, which is billable, and can be added to invoices the same way.  I rarely type something directly into an invoice.  Also, invoices in QBD do not have a markup column either.