I understand S Corps are flow through entities so if I am paying the net income on my personal taxes then can the S Corp pay for the taxes due? Also can the S Corp be able to deduct the taxes paid as a deduction?
can the S Corp pay for the taxes due?
Why? Why would the corporation, a separate legal entity, pay your personal obligations? Do you want to pierce the corporate veil? Because that's how you pierce the corporate veil.
Also can the S Corp be able to deduct the taxes paid as a deduction?
Of course not, how is it a deduction for the corporation? It's not a legitimate business expense.
The corporation can pay you a salary, and withhold taxes on your behalf from that salary. In fact, the corporation is required to do that if it's profitable (you're required to pay yourself a reasonable salary before taking distributions). But the corporation cannot and should not pay your personal obligations.