Hi and welcome to Just Answer!
As long as you are legally married - you may file a joint tax return if you both agree.
You may however file a separate tax return either as Married Filing separate (MFS) or as Head of Household (HOH) if you qualify.
To qualify for the HOH filing status - you should not live together with your spouse at least last six months of the year and have a qualified dependent living with you (your would qualify). You also need to provide more than haft of your household support.
If you do not feel comfortable to file a joint tax return - I suggest not to do so. Please be aware that if you do - you will be jointly liable for any tax liability resulted from that tax return.
However before you decide - I suggest to fill forms both ways and compare - it is possible that filing jointly will result in better refund, but there will be an issue how the refund will be divided - so you might want to an agreement before filing.
If you are using any tax preparation software - there should be an option to compare MFJ via MFS. If there is no difference or a difference is not substantial - you might better to file separately.
Please let me know if you need any help with estimations or any other clarification.
You may file amended tax return to change the filing status form MFS to MFJ - to do so - you should use the form 1040X - http://www.irs.gov/pub/irs-pdf/f1040x.pdf
Please be aware that you will not be amend your tax return to change to MFS after April 15, 2011.
The fact of filing a joint tax return may be used in the family court depending on your circumstances - but I am unclear if that will provide either of you any advantage as you are living separately any way. Generally the tax refund is divided equally unless there are other considerations.
If you will negotiate the amount of child support - that will likely based on yours and your spouse's income - and not on the fact of filing a joint tax return.
If your spouse's income is large enough - most likely he will benefit from filing a joint tax return - but to be precise - we need to estimate possible tax refund either way.
The main reason why you might want to amend your tax return - if your part of the tax refund will be larger. That is why I suggest to estimate before you could decide.