If you have both internal and reimbursable expenses, you should not select "Transfer Expense as Bill" in your setup table/Accounting Package in Manage. When this option is not selected, you can send over all types of expenses and they will come over to QuickBooks Online as an expense. From there, you can transfer your reimbursable expenses by cutting a check in QuickBooks.
If you would like to use the "Transfer Expense as Bill" option, you can complete the sync in two steps. First, check the "Transfer Expense as Bill" option. This will send over only the reimbursable expenses and leave behind the non-reimbursable expenses. Then you can uncheck "Transfer Expense as Bill" and transfer your non-reimbursable expenses.
Version 1.2 has improved the handling of expenses. You can find out more in this article. To get the latest version, reach out to email@example.com.