Yes, as long as the customer is on a transaction, (such as an Estimate, Invoice or Payment) then that customer will be transferred to your Quickbooks. If you've followed the steps on how to get QuickBooks integrated with MHelpDesk, the new customer you added in MHelpDesk will show once you send the new files to QuickBooks. To send your transactions to QuickBooks, go to "Transactions > Quickbooks View > Send To QuickBooks."
Don't have QuickBooks setup yet? Go to "Settings > Import From QuickBooks" to follow the directions on how to start the QuickBooks Integration.