If the purchase qualifies, the program will ask you for things like abstract fees, title fees and the such separately. Points is it's own thing. After entering all those amounts the program will add those things that qualify, to the cost basis of the home. It will also deduct those things from taxable income that qualify as a deduction.
Generally speaking, any fees associated with acquisition of the loan are deducted. For example, loan origination fees. Fees associated with the acquisition of the property are added to the cost basis of the property. For example, title transfer fees.
