The car allowance and the mileage allowance are two separate things. The car allowance is taxed as salary whatever you use the money for. The mileage allowance is to compensate you your private car travel.
Assuming you don't complete self-assessment tax returns, you should make a claim relief on the difference between what you receive from your employer and the maximum that you can receive tax free, the 45p and 25p rates you metioned.
You would normally use a P87
tax year to make your claim but as your total annual expense appears to be £2,500 or more, you may need to register fro self-assessment. Before you do that, however, call the number here
and ask if there is any way you can avoid completing a tax return claim year.
As you will see from the table here
, you can only claim as far back as 2010/11. There is more information on expense claims here
I hope this helps but let me know if you have any further questions.