what is the best way to handle reimbursed expenses?

This will reduce the total Auto Expense amount by the reimbursement.

If you regularly incur reimbursable expenses as an employee traveling on company business you may want to charge these expenses to a separate category and not mix it in with your personal expense categories.
For example, from many years ago I still have these categories in my Category List (I don't even know if Form 2106 is still valid):

You could create a category similar to the above Bus. Travel subcategory to track all your reimbursable expenses.
Once your company has reimbursed you for all your expenses, the category total should be reduced to $0.00