@KJC-CPA
RE: I would like to know the different methods available to import timesheets into QuickBooks.
You're right that there's the sync from the Intuit time product and, for Desktop, importing IIF files. If you have your time data in Excel and want to create reliable IIF files from it, use our BRC Timesheet Link. It'll create IIF files that follow the various QuickBooks rules, such as only recording time using payroll items that are set up on the employee.
RE: Now there are times when an employee will work under one particular pay code, but is paid at two different pay rates under that pay code, because they are working under different projects/customers. As of now, when that happens, we edit such paychecks manually because QuickBooks doesn't have the option for storing two different pay rates for a employee based on project/customer.
There is a way to handle this that may work for you. In the case where an employee earns two more more different rates of pay depending on what they're doing, set up and use different earnings items on the employee, each with its own rate. Then use those earnings items on time records. Later - when transferred to paychecks - the correct rate will be used by default, gathered from the employee record.
RE: If you use a timesheet application that stores the pay rates for employees on its end, is there a way to import completed paychecks directly into QuickBooks that already contain the hours and pay rates (and maybe even expense reimbursements)?
Unfortunately no. It actually isn't possible to import paychecks using any method.
