You can use either method - for recordkeeping purposes, I would suggest you add it to a separate line under the Registration fees.
In Massachusetts, this excise tax is considered a personal property tax, which is why it is deductible. So, you may see references to placing it under Deductions and Credits -> Cars and Other Things You Own -> Personal Property Taxes. Either one of these entry methods will get the amount to the right place on your tax return. Just don't enter it twice under both Personal Property Taxes and Registration fees