It will probably workout ok on your tax return. You will probably get a smaller refund after the child tax credits. The W4 is designed so you come out even at the end of the year, no tax due and no refund. If you want a bigger refund then change your W4 to Single and no dependents.
What you claim at work on the W4 doesn't have to match your actual tax return filing status. It's just to tell your employer how much to take out. You will get credit for all the withholding on your tax return. I'm married but claimed Single on the W4 to have more taxes taken out.