I was paid mileage included in T4A income. How do you separate to show this was a reimbursement not service income.

T4A income is self employed. You will report the car expenses on the T2125. 

No, you can not use a per KM rate. 

When you click on the income tab, go to self-employed summary and edit the business for created by the T4a.

Do I enter the amount under travel then on the T2125 or as vehicle expenses and have to log mileage etc. Which works out to less. The reimbursement for the mileage provided on the t4a should not be taxable but is recorded on the income line so I am not sure where on the t2125 to offset the amount

You will need to track your KMs and do the auto form.