How do I file if I'm married but separated from him. We are no long a couple but haven't file for divorce yet, how do I file when I'm head if household with one child.

In order to file as Head of Household you would have had to live apart from your spouse for the entire last 6 months of the year and you would have had to pay more than half the cost of keeping up your home for you and your qualifying child. 

If you did not live apart from your spouse for the entire last 6 months of the year or you do not meet the other criteria mentioned in the link above to file as Head of Household, you would file as Married Filing Separate.