Can I reimburse employee expenses like mileage, per diems and out of pocket expenses in payroll and be able to charge to the customer/project for expense tracking

The system doesn't allow payroll items to link directly to projects or customers. Payroll is a total company expense, so those reimbursements will not appear in your project tracking.

To avoid double-paying your employee, you can use a clearing account in your Chart of Accounts.

First, update your payroll reimbursement items so they point to this clearing account instead of a regular expense account.

Then, go to New and select Expense to log the project cost. On the first line, pick the actual expense category, select the project, and mark it billable. On the second line, select that same clearing account and enter the amount as a negative number.

Let me know if you need anything else.