Are Brokerage Fees deductible and if yes, are they part of the standard deduction or a separate input?

No. Starting Jan. 1, 2018, under the new Tax Cuts & Jobs Act, investment advisory fees (including account management fees) are NOT tax deductible, regardless of which funds are used to pay them.

not deductible for federal purposes but some states have different rules that could allow the deduction.  so what is your resident state?