State tax filing

Hi, I called FTB and I think I was even more confused, she says that both the federal and state filing status should be the same for our case. Since I have already filed the federal as MFJ, the state should also be MFJ. The representative said finally it will be the same amount because I should use Schedule CA (540NR) and we will only pay for the income made in CA. I went back to the MFJ return and add CA but this did not happen, somehow I ended up paying taxes in CA. Instead of getting a refund, I now owe money. Can you help me?