Estimated taxes for self employed quartley payments

Hi, 

On the 1040-ES form, I can use married filing jointly deductions, or the filing separately. 

However, I am self employed and my spouse is employed. 

Therefore, would you use MFJ deductions or filing separately? 

My spouse is asserting I should use the 12,500 deduction as otherwise it may result in me paying less than I actually should? 

Thanks in advance