If your partner have done his budgeting and he can show that he have enough money for living after paying the rent, loan repaymetns etc, that should be all right. ECO doesn't expect you to be millionaire after all. Your sponsor(partner) should of course, draw out a budget for them to see and provide a cover letter explaining the financial plan.
she only wants to know if being overdrawn on 3 of the 6 months bank statements given will make a difference to the visa?