1. yes, you can deduct registration fee for both, old and the new car.
2. yes - the 6% tax fee is the fee to use; to be deductible, the tax portion must be based on the value of the vehicle and be charged on a yearly basis. Registration, administrative, or emission testing fees, or tag or plate fees are not deductible for federal purposes. Often, your registration form will show separate lines for each item, be sure you deduct only the portion listed as for a vehicle tax - if the 6% tax fee that is a "tax" fee - then that is the amount to use.
Data entry in TurboTax:
Federal Taxes
Deductions Credits
Car and Other Things You Own
Car Registration Fees