If you're a cash-basis taxpayer (as most of us are), then you take off the registration fee in the year that you paid it, no matter how many years.
But, depending on the state you're in, you may not be able to deduct it. See your state's Department of Motor Vehicles webpage for more.
If you're taking off the registration fee, you take it as a deduction on Schedule A.
Go to Deductions & Credits
Go to Cars and Other Things you Own
Go to Car Registration Fees.